Differential Expression analyses
Thomas Dobrenel and Nicolas Delhomme
2019-11-21
1 Setup
- Working dir
setwd("/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR")- Libraries
suppressPackageStartupMessages(library(data.table))
suppressPackageStartupMessages(library(DESeq2))
suppressPackageStartupMessages(library(gplots))
suppressPackageStartupMessages(library(hyperSpec))
suppressPackageStartupMessages(library(LSD))
suppressPackageStartupMessages(library(magrittr))
suppressPackageStartupMessages(library(matrixStats))
suppressPackageStartupMessages(library(RColorBrewer))
suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(VennDiagram))- Helpers
suppressPackageStartupMessages(source("~/Git/UPSCb/UPSCb-common/src/R/gopher.R"))- Graphics
hpal <- colorRampPalette(c("blue","white","red"))(100)
pal <- brewer.pal(9,"Paired") #require package RColorBrewer
mar <- par("mar")
suppressPackageStartupMessages(source("~/Git/UPSCb/UPSCb-common/src/R/volcanoPlot.R"))- Cutoff As of Schurch et al., RNA, 2016
lfc <- 0.5
FDR <- 0.01- Raw data
load("analysis_Tom/counts.rda")- Selection of the validated samples
samples %<>% filter(!grepl("P11554_1",SciLifeID)) %>%
filter(Timepoint!=24) %>%
filter(Nutrition!="PKS") %>%
mutate(Timepoint,Timepoint=factor(paste0("T",Timepoint))) %>%
mutate(Nutrition,Nutrition=relevel(Nutrition,"NPS")) %>%
mutate(AZD,AZD=relevel(AZD,"DMSO"))
kg <- kg[,match(samples$SciLifeID,colnames(kg))]- Validation
stopifnot(all(samples$SciLifeID == colnames(kg)))
stopifnot(all(samples$Batch == "B2"))2 Differential expression based on the nutrition and treatment at T6
2.1 Filtration of samples based on timepoint
sel_T6 <- samples$Timepoint == "T6"
suppressMessages(dds_T6 <- DESeqDataSetFromMatrix(
countData = kg[,sel_T6],
colData = samples[sel_T6,],
design = ~ Nutrition * AZD ))2.2 Differential expression analysis
dds_T6 <- DESeq(dds_T6)## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing2.3 Variance Stabilising Transformation
2.3.1 Perform a Variance Stabilizing Transformation for plotting
vst_T6 <- varianceStabilizingTransformation(dds_T6,blind=FALSE)
vsd_T6 <- assay(vst_T6)
vsd_T6 <- vsd_T6 - min(vsd_T6)2.3.2 Calculation of fold change compared to NPS_DMSO at 6 hrs
colAvg_T6 <- sapply(split.data.frame(t(vsd_T6),f = droplevels(samples$Conditions[sel_T6])),colMeans)
fc_T6 <- colAvg_T6[,- match("6_NPS_DMSO",colnames(colAvg_T6))] - colAvg_T6[,"6_NPS_DMSO"]
fc2_T6 <- vsd_T6 - colAvg_T6[,"6_NPS_DMSO"]
range(fc_T6)## [1] -3.170596 5.545431fc_T6[fc_T6>2] <- 2 ; fc_T6[fc_T6 < -2] <- -2
fc2_T6[fc2_T6>2] <- 2 ; fc2_T6[fc2_T6 < -2] <- -2
#range(fc_T6)2.4 Contrasts to NPS_DMSO
The contrast by default is the first one (not Intercept)
resultsNames(dds_T6)## [1] "Intercept" "Nutrition_NP_vs_NPS" "Nutrition_NS_vs_NPS"
## [4] "AZD_AZD_vs_DMSO" "NutritionNP.AZDAZD" "NutritionNS.AZDAZD"2.4.1 Nutrition effect of carbon starvation
2.4.1.1 Extraction of the results from the DESeq analysis
res_Suc <- results(dds_T6,name = "Nutrition_NP_vs_NPS")
# res <- results(dds,contrast = c(Nutrition","NP","NS"))
# res <- results(dds,contrast = list("Nutrition_NP_vs_NPS","Nutrition_NS_vs_NPS"))
# res <- results(dds,contrast = c(0,1,-1,0,0,0,0,0,0) # NP vs. NS
cutoffs_Suc <- abs(res_Suc$log2FoldChange) >= lfc & ! is.na(res_Suc$padj) & res_Suc$padj <= FDR
cutoff1_Suc <- res_Suc$log2FoldChange >= lfc & ! is.na(res_Suc$padj) & res_Suc$padj <= FDR
cutoff2_Suc <- res_Suc$log2FoldChange <= -lfc & ! is.na(res_Suc$padj) & res_Suc$padj <= FDR
SucStarvEffect <- rownames(res_Suc[cutoffs_Suc,])
SucStarvLow <- rownames(res_Suc[cutoff2_Suc,])
SucStarvHigh <- rownames(res_Suc[cutoff1_Suc,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs_Suc)))## There are 1693 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1_Suc)))## There are 709 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2_Suc)))## There are 984 genes that are repressed2.4.1.2 MA plot
DESeq2::plotMA(res_Suc)
2.4.1.3 Volcano plot
volcanoPlot(res_Suc)
svg(filename="VolcanoSucStarv.svg",
width=10,
height=8,
pointsize=12)
volcanoPlot(res_Suc)
dev.off()## png
## 22.4.1.4 Heatmap
hm <- heatmap.2(t(scale(t(vsd_T6[cutoffs_Suc,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
svg(filename="HeatMapSucStarv.svg",
width=10,
height=8,
pointsize=12)
hm <- heatmap.2(t(scale(t(vsd_T6[cutoffs_Suc,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
dev.off()## png
## 22.4.1.5 Enrichment analysis
2.4.1.5.1 Downregulated genes
EnrSucLow <- gopher(SucStarvLow,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## Loading required package: jsonlite##
## Attaching package: 'jsonlite'## The following object is masked from 'package:purrr':
##
## flatten## No enrichments found in task: mapmanEnrSucLow$go$name## [1] "response to stimulus"
## [2] "thylakoid"
## [3] "extracellular region"
## [4] "secondary metabolic process"
## [5] "pyridine-containing compound metabolic process"
## [6] "plastid"
## [7] "vacuole"
## [8] "cofactor metabolic process"
## [9] "carbohydrate metabolic process"
## [10] "fluid transport"
## [11] "response to red light"
## [12] "drug metabolic process"
## [13] "flavonoid metabolic process"
## [14] "response to inorganic substance"
## [15] "glucose 6-phosphate metabolic process"
## [16] "apoplast"
## [17] "generation of precursor metabolites and energy"
## [18] "cytoplasm"
## [19] "membrane"
## [20] "PSII associated light-harvesting complex II catabolic process"
## [21] "plastid organization"
## [22] "lipid metabolic process"
## [23] "tetrapyrrole metabolic process"
## [24] "photosynthesis"
## [25] "aging"
## [26] "endomembrane system organization"
## [27] "protein localization to membrane"
## [28] "response to far red light"
## [29] "catabolic process"
## [30] "reactive oxygen species metabolic process"
## [31] "response to blue light"
## [32] "ion transport"
## [33] "starch metabolic process"
## [34] "pigment metabolic process"
## [35] "cellular aldehyde metabolic process"
## [36] "response to chemical"
## [37] "oligosaccharide metabolic process"
## [38] "carbohydrate derivative metabolic process"
## [39] "inorganic anion transport"
## [40] "catalytic activity"
## [41] "positive regulation of molecular function"
## [42] "cell death"
## [43] "cell periphery"
## [44] "sulfur compound metabolic process"
## [45] "glycogen debranching enzyme activity"
## [46] "oxidoreductase activity"
## [47] "plastid part"
## [48] "stromule"
## [49] "response to acid chemical"
## [50] "single-stranded RNA binding"
## [51] "serine family amino acid metabolic process"
## [52] "regulation of protein metabolic process"
## [53] "envelope"
## [54] "liposaccharide metabolic process"
## [55] "cold acclimation"
## [56] "cellular response to environmental stimulus"
## [57] "biological regulation"
## [58] "organonitrogen compound metabolic process"
## [59] "regulation of molecular function"
## [60] "immune system process"
## [61] "glutamine metabolic process"
## [62] "positive regulation of biological process"
## [63] "de-etiolation"
## [64] "oxidoreduction coenzyme metabolic process"
## [65] "tetrapyrrole binding"
## [66] "organelle part"
## [67] "rhythmic process"
## [68] "light-harvesting complex"
## [69] "ureide metabolic process"
## [70] "oxidoreductase activity, acting on single donors with incorporation of molecular oxygen"
## [71] "cell communication"
## [72] "response to extracellular stimulus"
## [73] "rRNA metabolic process"
## [74] "glycosyl compound metabolic process"
## [75] "cellular homeostasis"
## [76] "response to osmotic stress"
## [77] "UDP-glycosyltransferase activity"
## [78] "organelle subcompartment"
## [79] "response to desiccation"
## [80] "small molecule metabolic process"
## [81] "RNA metabolic process"
## [82] "regulation of seedling development"
## [83] "microbody"
## [84] "chromatin assembly or disassembly"
## [85] "transmembrane transporter activity"EnrSucLow$kegg$id## [1] "3.4.22.1" "2.6.1.4" "1.18.1.2" "2.4.1.14" "2.4.1.91"
## [6] "1.14.13.90" "2.4.1.25" "2.4.1.13" "1.14.13.173" "1.1.1.49"
## [11] "2.3.2.2" "3.4.22.16" "2.4.1.1" "1.1.3.15" "3.4.16.5"
## [16] "3.4.22.41" "2.6.1.44" "1.7.1.1"EnrSucLow$pfam$name## [1] "zinc-finger of the FCS-type, C2-C2"
## [2] "Sucrose synthase"
## [3] "Papain family cysteine protease"
## [4] "Alpha amylase, catalytic domain"
## [5] "Carbohydrate-binding module 48 (Isoamylase N-terminal domain)"
## [6] "NAF domain"
## [7] "FMN-dependent dehydrogenase"
## [8] "Peptidase family C1 propeptide"
## [9] "Universal stress protein family"
## [10] "UDP-glucoronosyl and UDP-glucosyl transferase"
## [11] "No apical meristem (NAM) protein"
## [12] "Oxidoreductase NAD-binding domain"
## [13] "PB1 domain"
## [14] "Dehydrin"
## [15] "Cystatin domain"
## [16] "WD40-like Beta Propeller Repeat"
## [17] "Cathepsin propeptide inhibitor domain (I29)"
## [18] "Sucrose-6F-phosphate phosphohydrolase"
## [19] "Thiolase, N-terminal domain"
## [20] "Thiolase, C-terminal domain"
## [21] "Glycosyl transferases group 1"
## [22] "Cold acclimation protein WCOR413"
## [23] "Glucose-6-phosphate dehydrogenase, C-terminal domain"
## [24] "Glucose-6-phosphate dehydrogenase, NAD binding domain"
## [25] "4-alpha-glucanotransferase"
## [26] "Ion channel"
## [27] "HPP family"
## [28] "Domain of unknown function (DUF4210)"
## [29] "Chromosome segregation during meiosis"
## [30] "Carbohydrate phosphorylase"
## [31] "Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain"
## [32] "Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain"
## [33] "Major intrinsic protein"write.table(data.frame(EnrSucLow$go$id, EnrSucLow$go$padj), file = "GeneOntologySucLow.txt", sep = "\t",
row.names = FALSE)2.4.1.5.2 Upregulated genes
EnrSucHigh <- gopher(SucStarvHigh,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmanEnrSucHigh$go$name## [1] "cell periphery"
## [2] "extracellular region"
## [3] "cell wall organization or biogenesis"
## [4] "cell junction"
## [5] "symplast"
## [6] "external encapsulating structure organization"
## [7] "hydrolase activity, acting on glycosyl bonds"
## [8] "membrane"
## [9] "steroid metabolic process"
## [10] "intrinsic component of membrane"
## [11] "external encapsulating structure"
## [12] "growth"
## [13] "plant-type cell wall"
## [14] "carbohydrate metabolic process"
## [15] "syncytium formation"
## [16] "endomembrane system"
## [17] "anchored component of membrane"
## [18] "protein polymerization"
## [19] "vesicle"
## [20] "root system development"
## [21] "organic hydroxy compound metabolic process"
## [22] "plant-type cell wall loosening"
## [23] "response to mechanical stimulus"
## [24] "plant epidermal cell differentiation"
## [25] "multidimensional cell growth"
## [26] "ER body"
## [27] "nucleoside bisphosphate metabolic process"
## [28] "pigmentation"
## [29] "tubulin complex"
## [30] "galacturonan metabolic process"
## [31] "polygalacturonate 4-alpha-galacturonosyltransferase activity"
## [32] "Golgi apparatus"
## [33] "regulation of biological quality"
## [34] "cytoskeleton organization"
## [35] "ER body organization"
## [36] "response to wounding"
## [37] "cell development"
## [38] "oligopeptide transport"
## [39] "carbon-oxygen lyase activity, acting on polysaccharides"
## [40] "transferase activity, transferring glycosyl groups"
## [41] "organonitrogen compound metabolic process"
## [42] "vacuole"
## [43] "indole-containing compound metabolic process"
## [44] "meristem maintenance"
## [45] "developmental maturation"
## [46] "structural constituent of cytoskeleton"
## [47] "structural constituent of cell wall"
## [48] "tissue development"
## [49] "hydrolase activity"
## [50] "response to UV"
## [51] "regulation of meristem development"EnrSucHigh$kegg$id## [1] "2.4.1.207" "3.2.1.4" "3.4.23.12" "2.4.2.39" "1.10.3.3" "4.2.2.2"
## [7] "3.2.1.151" "2.4.1.43" "3.1.1.11" "1.13.99.1" "3.2.1.39" "1.10.3.2"EnrSucHigh$pfam$name## [1] "Glycosyl hydrolases family 16"
## [2] "Xyloglucan endo-transglycosylase (XET) C-terminus"
## [3] "Fasciclin domain"
## [4] "Glycosyl hydrolase family 9"
## [5] "Protein of unknown function (DUF1005)"
## [6] "Leucine rich repeat N-terminal domain"
## [7] "Pollen allergen"
## [8] "Lytic transglycolase"
## [9] "Pectinacetylesterase"
## [10] "Multicopper oxidase"
## [11] "Arabinogalactan peptide"
## [12] "Multicopper oxidase"
## [13] "Multicopper oxidase"
## [14] "Eukaryotic aspartyl protease"
## [15] "HAD superfamily, subfamily IIIB (Acid phosphatase)"
## [16] "Tubulin C-terminal domain"
## [17] "Pectate lyase"
## [18] "Glycosyl transferase family group 2"
## [19] "Tubulin/FtsZ family, GTPase domain"
## [20] "Phosphate-induced protein 1 conserved region"
## [21] "Protein of unknown function (DUF642)"
## [22] "Glycosyl hydrolases family 17"
## [23] "Jacalin-like lectin domain"
## [24] "X8 domain"
## [25] "Putative S-adenosyl-L-methionine-dependent methyltransferase"
## [26] "Xylanase inhibitor N-terminal"
## [27] "Pectinesterase"
## [28] "galactosyl transferase GMA12/MNN10 family"
## [29] "Leucine rich repeat"
## [30] "Rapid ALkalinization Factor (RALF)"
## [31] "C1 domain"
## [32] "Domain of unknown function (DUF588)"
## [33] "Ndr family"
## [34] "Myo-inositol oxygenase"
## [35] "(Dead): PF07649"write.table(data.frame(EnrSucHigh$go$id, EnrSucHigh$go$padj), file = "GeneOntologySucHigh.txt", sep = "\t",
row.names = FALSE)2.4.2 Nutrition effect of phosphorus starvation
#’ #### Extraction of the results from the DESeq analysis
res_Pi <- results(dds_T6,name = "Nutrition_NS_vs_NPS")
# res <- results(dds,contrast = c(Nutrition","NP","NS"))
# res <- results(dds,contrast = list("Nutrition_NP_vs_NPS","Nutrition_NS_vs_NPS"))
# res <- results(dds,contrast = c(0,1,-1,0,0,0,0,0,0) # NP vs. NS
cutoffs_Pi <- abs(res_Pi$log2FoldChange) >= lfc & ! is.na(res_Pi$padj) & res_Pi$padj <= FDR
cutoff1_Pi <- res_Pi$log2FoldChange >= lfc & ! is.na(res_Pi$padj) & res_Pi$padj <= FDR
cutoff2_Pi <- res_Pi$log2FoldChange <= -lfc & ! is.na(res_Pi$padj) & res_Pi$padj <= FDR
PiStarvEffect <- rownames(res_Pi[cutoffs_Pi,])
PiStarvLow <- rownames(res_Pi[cutoff2_Pi,])
PiStarvHigh <- rownames(res_Pi[cutoff1_Pi,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs_Pi)))## There are 6994 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1_Pi)))## There are 3173 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2_Pi)))## There are 3821 genes that are repressed2.4.2.1 MA plot
DESeq2::plotMA(res_Pi)
2.4.2.2 Volcano plot
volcanoPlot(res_Pi)
svg(filename="VolcanoPiStarv.svg",
width=10,
height=8,
pointsize=12)
volcanoPlot(res_Pi)
dev.off()## png
## 22.4.2.3 Heatmap
2.4.2.3.1 Z-score
hm <- heatmap.2(t(scale(t(vsd_T6[cutoffs_Pi,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
svg(filename="HeatMapPiStarv.svg",
width=10,
height=8,
pointsize=12)
hm <- heatmap.2(t(scale(t(vsd_T6[cutoffs_Pi,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
dev.off()## png
## 22.4.2.4 Enrichment analysis
2.4.2.4.1 Downregulated genes
EnrPiLow <- gopher(PiStarvLow,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmanEnrPiLow$go$name## [1] "non-membrane-bounded organelle"
## [2] "methylation"
## [3] "structural molecule activity"
## [4] "cytosolic part"
## [5] "protein-containing complex"
## [6] "cellular component organization or biogenesis"
## [7] "membrane-enclosed lumen"
## [8] "protein alkylation"
## [9] "nitrogen compound metabolic process"
## [10] "ribonucleoprotein complex"
## [11] "organelle part"
## [12] "cellular nitrogen compound metabolic process"
## [13] "ribonucleoprotein complex biogenesis"
## [14] "heterocycle metabolic process"
## [15] "cellular amide metabolic process"
## [16] "cell proliferation"
## [17] "peptidyl-amino acid modification"
## [18] "pyrimidine-containing compound metabolic process"
## [19] "cellular aromatic compound metabolic process"
## [20] "mitochondrial transport"
## [21] "organic cyclic compound metabolic process"
## [22] "cell cycle"
## [23] "DNA metabolic process"
## [24] "nuclear transport"
## [25] "macromolecule metabolic process"
## [26] "gene silencing"
## [27] "protein localization to organelle"
## [28] "metabolic process"
## [29] "cellular process"
## [30] "cell division"
## [31] "cytosol"
## [32] "organelle"
## [33] "structural constituent of ribosome"
## [34] "cellular response to DNA damage stimulus"
## [35] "organelle organization"
## [36] "ncRNA metabolic process"
## [37] "RNA modification"
## [38] "regulation of gene expression, epigenetic"
## [39] "reproduction"
## [40] "protein-containing complex localization"
## [41] "catalytic activity, acting on RNA"
## [42] "primary metabolic process"
## [43] "gene expression"
## [44] "embryo sac development"
## [45] "multi-organism reproductive process"
## [46] "cellular localization"
## [47] "heterocyclic compound binding"
## [48] "DNA replication"
## [49] "organic cyclic compound binding"
## [50] "chromosome organization"
## [51] "post-embryonic plant morphogenesis"
## [52] "shoot system development"
## [53] "multicellular organismal process"
## [54] "protein localization to nucleus"
## [55] "isoprenoid metabolic process"
## [56] "hydrolase activity, acting on acid anhydrides"
## [57] "cellular process involved in reproduction in multicellular organism"
## [58] "RNA localization"
## [59] "cell"
## [60] "amide transport"
## [61] "mitochondrion organization"
## [62] "ribonucleoprotein complex localization"
## [63] "RNA processing"
## [64] "protein localization to mitochondrion"
## [65] "organophosphate metabolic process"
## [66] "flower calyx development"
## [67] "macromolecule localization"
## [68] "cytoplasmic part"
## [69] "cell cycle phase transition"
## [70] "microtubule-based process"
## [71] "anatomical structure formation involved in morphogenesis"
## [72] "RNA binding"
## [73] "catalytic activity, acting on DNA"
## [74] "peptide metabolic process"
## [75] "chromosome segregation"
## [76] "developmental process"
## [77] "external encapsulating structure"
## [78] "gametophyte development"
## [79] "nucleotidyltransferase activity"
## [80] "nucleobase-containing compound metabolic process"
## [81] "isopentenyl diphosphate metabolic process"
## [82] "organic substance metabolic process"
## [83] "regulation of cell cycle"
## [84] "negative regulation of metabolic process"
## [85] "regulation of DNA metabolic process"
## [86] "pyruvate metabolic process"
## [87] "nuclear part"
## [88] "DNA replication initiation"
## [89] "biosynthetic process"
## [90] "DNA-dependent ATPase activity"
## [91] "cell junction"
## [92] "envelope"
## [93] "symplast"
## [94] "nucleic acid transport"
## [95] "response to red or far red light"
## [96] "transferase activity, transferring one-carbon groups"
## [97] "organic substance transport"
## [98] "nuclease activity"
## [99] "plastid"
## [100] "response to cytokinin"
## [101] "corolla development"
## [102] "nucleoid"
## [103] "protein import"
## [104] "regulation of reproductive process"
## [105] "anion binding"
## [106] "nitrogen compound transport"
## [107] "organelle assembly"
## [108] "nucleobase-containing compound transport"
## [109] "kinase regulator activity"
## [110] "negative regulation of gene expression, epigenetic"
## [111] "binding"
## [112] "helicase activity"
## [113] "multicellular organism reproduction"
## [114] "thylakoid"
## [115] "copper ion binding"
## [116] "anatomical structure homeostasis"
## [117] "macromolecule modification"
## [118] "plastid transcription"
## [119] "protein modification by small protein conjugation"
## [120] "protein deubiquitination"
## [121] "nucleobase-containing small molecule metabolic process"
## [122] "intracellular"
## [123] "double-strand break repair"
## [124] "female gamete generation"
## [125] "reproductive system development"
## [126] "anchored component of membrane"
## [127] "ribosome"
## [128] "ligase activity"
## [129] "apoplast"
## [130] "response to ionizing radiation"
## [131] "cellular metabolic process"
## [132] "double-stranded DNA binding"
## [133] "histone H3-K9 modification"
## [134] "regulation of biological process"
## [135] "post-embryonic plant organ development"
## [136] "regulation of multicellular organismal process"
## [137] "protein transporter activity"
## [138] "plastid localization"
## [139] "response to virus"
## [140] "import into nucleus"
## [141] "nucleobase-containing compound kinase activity"
## [142] "mitochondrion"
## [143] "carbohydrate derivative binding"
## [144] "regulation of anatomical structure size"
## [145] "regulation of developmental process"
## [146] "multicellular organism development"
## [147] "regulation of growth"
## [148] "TIM23 mitochondrial import inner membrane translocase complex"
## [149] "organelle fusion"
## [150] "response to carbohydrate"
## [151] "single-stranded DNA binding"
## [152] "phosphatidylglycerol metabolic process"
## [153] "protein localization"
## [154] "carbon-oxygen lyase activity, acting on polysaccharides"
## [155] "DNA modification"
## [156] "plant organ formation"
## [157] "hydrolase activity"
## [158] "ribosomal small subunit biogenesis"
## [159] "macromolecule transmembrane transporter activity"
## [160] "response to radiation"
## [161] "RNA interference"
## [162] "RNA splicing, via transesterification reactions"
## [163] "peptidyl-lysine modification"
## [164] "posttranscriptional regulation of gene expression"
## [165] "ribonucleotide metabolic process"
## [166] "megagametogenesis"
## [167] "anion transmembrane transporter activity"
## [168] "negative regulation of biological process"
## [169] "lipid biosynthetic process"
## [170] "damaged DNA binding"
## [171] "RNA phosphodiester bond hydrolysis"
## [172] "nucleus organization"
## [173] "transferase activity, transferring pentosyl groups"
## [174] "pigment biosynthetic process"
## [175] "transferase complex"
## [176] "adenyl nucleotide binding"
## [177] "pseudouridine synthase activity"
## [178] "multidimensional cell growth"
## [179] "omega-3 fatty acid desaturase activity"
## [180] "positive regulation of cellular process"
## [181] "cell surface receptor signaling pathway"
## [182] "lysine metabolic process"
## [183] "response to metal ion"
## [184] "DNA secondary structure binding"
## [185] "response to cyclopentenone"
## [186] "electron transport chain"
## [187] "cell-cell signaling"
## [188] "post-embryonic development"
## [189] "establishment of organelle localization"
## [190] "organic substance biosynthetic process"
## [191] "isomerase activity"
## [192] "plant-type cell wall organization or biogenesis"
## [193] "protein localization to chloroplast"
## [194] "phosphorus metabolic process"
## [195] "sulfur compound transmembrane transporter activity"
## [196] "mitotic cell cycle"
## [197] "plant epidermis morphogenesis"
## [198] "translation factor activity, RNA binding"
## [199] "ribonucleoprotein complex subunit organization"
## [200] "protein-DNA complex subunit organization"
## [201] "N-methyltransferase activity"
## [202] "covalent chromatin modification"
## [203] "nucleic acid phosphodiester bond hydrolysis"
## [204] "purine-containing compound salvage"
## [205] "plastid stroma"
## [206] "plasma membrane part"
## [207] "negative gravitropism"
## [208] "cellular amino acid biosynthetic process"
## [209] "DNA conformation change"
## [210] "small molecule binding"
## [211] "tubulin complex"
## [212] "regulation of nitrogen compound metabolic process"
## [213] "cyclin-dependent protein kinase activity"
## [214] "amide transmembrane transporter activity"
## [215] "adenylyl-sulfate reductase activity"
## [216] "coenzyme metabolic process"EnrPiLow$kegg$id## [1] "3.6.4.13" "2.7.7.6" "3.6.5.3" "3.6.4.12" "2.7.7.7" "3.6.4.4"
## [7] "2.1.1.125" "3.6.4.5" "4.2.2.2" "2.1.1.43" "3.1.26.5" "5.99.1.3"EnrPiLow$pfam$name## [1] "PPR repeat"
## [2] "PPR repeat family"
## [3] "DYW family of nucleic acid deaminases"
## [4] "Core histone H2A/H2B/H3/H4"
## [5] "Helicase conserved C-terminal domain"
## [6] "TCP-1/cpn60 chaperonin family"
## [7] "Elongation factor Tu GTP binding domain"
## [8] "Pentatricopeptide repeat domain"
## [9] "DEAD/DEAH box helicase"
## [10] "50S ribosome-binding GTPase"
## [11] "Elongation factor Tu domain 2"
## [12] "Cyclin, C-terminal domain"
## [13] "Ribosomal protein L1p/L10e family"
## [14] "60s Acidic ribosomal protein"
## [15] "3 exoribonuclease family, domain 2"
## [16] "Kinesin motor domain"
## [17] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [18] "S1 RNA binding domain"
## [19] "3 exoribonuclease family, domain 1"
## [20] "Cyclin, N-terminal domain"
## [21] "C-terminus of histone H2A"
## [22] "LSM domain"
## [23] "Type III restriction enzyme, res subunit"
## [24] "Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A"
## [25] "Plant organelle RNA recognition domain"
## [26] "Mitochondrial glycoprotein"
## [27] "Ribosomal protein L13"
## [28] "Brix domain"
## [29] "MCM P-loop domain"
## [30] "PPR repeat"
## [31] "Zinc knuckle"
## [32] "MCM N-terminal domain"
## [33] "Ribosomal protein L30p/L7e"
## [34] "NAC domain"
## [35] "Ribosomal protein S9/S16"
## [36] "KH domain"
## [37] "Ribosomal protein S5, N-terminal domain"
## [38] "MutS domain I"
## [39] "ribosomal L5P family C-terminus"
## [40] "Ribosomal protein L5"
## [41] "WD domain, G-beta repeat"
## [42] "Ribosomal protein S5, C-terminal domain"
## [43] "tRNA synthetases class I (I, L, M and V)"
## [44] "Ribosomal protein L41"
## [45] "RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)"
## [46] "Calponin homology (CH) domain"
## [47] "mTERF"
## [48] "Elongation factor Tu C-terminal domain"
## [49] "Centromere kinetochore component CENP-T histone fold"
## [50] "Anticodon-binding domain of tRNA"
## [51] "16S rRNA methyltransferase RsmB/F"
## [52] "Ribosomal protein L3"
## [53] "Ribosomal protein L21e"
## [54] "DEAD_2"
## [55] "Translation initiation factor eIF3 subunit 135"
## [56] "Nucleosome assembly protein (NAP)"
## [57] "S25 ribosomal protein"
## [58] "MutS domain II"
## [59] "Ribosomal L30 N-terminal domain"
## [60] "Protein of unknown function (DUF629)"
## [61] "Ribosomal protein L4/L1 family"
## [62] "Ribosomal protein L10"
## [63] "FtsJ-like methyltransferase"
## [64] "Ribosomal protein L19e"
## [65] "Tubulin/FtsZ family, GTPase domain"
## [66] "Tubulin C-terminal domain"
## [67] "MutS domain III"
## [68] "Ribosomal S17"
## [69] "Domain of unknown function (DUF3523)"
## [70] "Ribosomal protein L14p/L23e"
## [71] "Dip2/Utp12 Family"
## [72] "Importin-beta N-terminal domain"
## [73] "Phosphoribosyl transferase domain"
## [74] "Mitochondrial function, CLU-N-term"
## [75] "Replication factor C C-terminal domain"
## [76] "Protein of unknown function (DUF627)"
## [77] "Tetratricopeptide repeat"
## [78] "N2,N2-dimethylguanosine tRNA methyltransferase"
## [79] "NOP5NT (NUC127) domain"
## [80] "Tim10/DDP family zinc finger"
## [81] "S4 domain"
## [82] "Pectate lyase"
## [83] "MutS domain V"
## [84] "Elongation factor G C-terminus"
## [85] "Elongation factor G, domain IV"
## [86] "Hsp90 protein"
## [87] "tRNA pseudouridine synthase"
## [88] "OB-fold nucleic acid binding domain"
## [89] "KOW motif"
## [90] "Protein of unknown function (DUF724)"
## [91] "Ubiquitin carboxyl-terminal hydrolase"write.table(data.frame(EnrPiLow$go$id, EnrPiLow$go$padj), file = "GeneOntologyPiLow.txt", sep = "\t",
row.names = FALSE)2.4.2.4.2 Upregulated genes
EnrPiHigh <- gopher(PiStarvHigh,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: kegg## No enrichments found in task: mapmanEnrPiHigh$go$name## [1] "response to stimulus"
## [2] "catabolic process"
## [3] "liposaccharide metabolic process"
## [4] "lipid metabolic process"
## [5] "cell communication"
## [6] "protein localization to vacuole"
## [7] "endomembrane system organization"
## [8] "localization"
## [9] "membrane lipid metabolic process"
## [10] "aging"
## [11] "benzene-containing compound metabolic process"
## [12] "vacuole"
## [13] "secondary metabolic process"
## [14] "cellular response to phosphate starvation"
## [15] "endomembrane system"
## [16] "cytoplasm"
## [17] "process utilizing autophagic mechanism"
## [18] "cell periphery"
## [19] "vacuolar transport"
## [20] "cell death"
## [21] "response to acid chemical"
## [22] "membrane"
## [23] "postreplication repair"
## [24] "catalytic activity"
## [25] "nucleoside diphosphate metabolic process"
## [26] "response to stress"
## [27] "vesicle-mediated transport"
## [28] "carbohydrate derivative biosynthetic process"
## [29] "response to inorganic substance"
## [30] "vacuole organization"
## [31] "peroxisome organization"
## [32] "flavonoid metabolic process"
## [33] "nucleoside monophosphate metabolic process"
## [34] "small molecule metabolic process"
## [35] "hydrolase activity, acting on ester bonds"
## [36] "cellular response to external stimulus"
## [37] "response to extracellular stimulus"
## [38] "nucleoside triphosphate metabolic process"
## [39] "response to external stimulus"
## [40] "carbohydrate derivative metabolic process"
## [41] "small molecule biosynthetic process"
## [42] "drug metabolic process"
## [43] "response to alcohol"
## [44] "response to fungus"
## [45] "response to oxygen-containing compound"
## [46] "organonitrogen compound metabolic process"
## [47] "protein targeting"
## [48] "response to osmotic stress"
## [49] "DNA binding"
## [50] "organic hydroxy compound metabolic process"
## [51] "regulation of response to stimulus"
## [52] "microbody"
## [53] "response to lipid"
## [54] "pigment catabolic process"
## [55] "stomatal movement"
## [56] "immune system process"
## [57] "monocarboxylic acid metabolic process"
## [58] "plant epidermal cell differentiation"
## [59] "phosphoric ester hydrolase activity"
## [60] "proteasome assembly"
## [61] "response to symbiont"
## [62] "organic acid metabolic process"
## [63] "response to ethylene"
## [64] "carbohydrate metabolic process"
## [65] "regulation of immune system process"
## [66] "protein modification process"
## [67] "cellular macromolecule metabolic process"
## [68] "ATPase activity, coupled to movement of substances"
## [69] "multi-organism process"
## [70] "signaling"
## [71] "lipid modification"
## [72] "pollen development"
## [73] "response to light stimulus"
## [74] "cytoskeleton"
## [75] "oxidation-reduction process"
## [76] "tetrapyrrole metabolic process"
## [77] "response to wounding"
## [78] "transporter activity"
## [79] "tethering complex"
## [80] "polyol metabolic process"
## [81] "indole-containing compound metabolic process"
## [82] "protein binding"
## [83] "defense response, incompatible interaction"
## [84] "oligosaccharide biosynthetic process"
## [85] "fatty acid metabolic process"
## [86] "aromatic compound biosynthetic process"
## [87] "regulation of seedling development"
## [88] "guanyl nucleotide binding"
## [89] "protein localization"
## [90] "adenylyltransferase activity"
## [91] "nucleoside binding"
## [92] "intracellular signal transduction"
## [93] "response to temperature stimulus"
## [94] "phosphate ion transmembrane transporter activity"
## [95] "response to antibiotic"
## [96] "glycoprotein metabolic process"
## [97] "phosphatidylinositol metabolic process"
## [98] "regulation of photosynthesis"
## [99] "lipoprotein metabolic process"
## [100] "glycosylation"
## [101] "cell development"
## [102] "root hair cell development"
## [103] "response to toxic substance"
## [104] "response to biotic stimulus"
## [105] "male gamete generation"
## [106] "cellular lipid metabolic process"
## [107] "intramolecular transferase activity, phosphotransferases"
## [108] "8-methylthiopropyl glucosinolate S-oxygenase activity"
## [109] "purine-containing compound metabolic process"
## [110] "sucrose metabolic process"
## [111] "response to chemical"
## [112] "proteolysis"
## [113] "cellular response to environmental stimulus"
## [114] "regulation of seed development"
## [115] "signal transduction by protein phosphorylation"
## [116] "N,N-dimethylaniline monooxygenase activity"
## [117] "negative regulation of developmental process"
## [118] "oxidoreductase activity"
## [119] "root system development"
## [120] "ER-nucleus signaling pathway"
## [121] "nucleobase-containing small molecule biosynthetic process"
## [122] "heterocycle biosynthetic process"
## [123] "cofactor catabolic process"
## [124] "nucleotide phosphorylation"
## [125] "ion binding"
## [126] "N-terminal protein amino acid modification"
## [127] "regulation of microtubule-based process"
## [128] "response to host"
## [129] "regulation of hormone levels"
## [130] "negative regulation of multicellular organismal process"
## [131] "cytosol"
## [132] "regulation of gene silencing"
## [133] "RNA splicing, via endonucleolytic cleavage and ligation"
## [134] "pyridine-containing compound metabolic process"
## [135] "cell wall thickening"
## [136] "response to starvation"
## [137] "lipid droplet"
## [138] "organic cyclic compound biosynthetic process"
## [139] "immune response"
## [140] "de-etiolation"
## [141] "maintenance of location in cell"EnrPiHigh$kegg$id## NULLEnrPiHigh$pfam$name## [1] "Purple acid Phosphatase, N-terminal domain"
## [2] "Iron/zinc purple acid phosphatase-like protein C"
## [3] "Calcineurin-like phosphoesterase"
## [4] "Major Facilitator Superfamily"
## [5] "Ubiquitin-like autophagy protein Apg12"
## [6] "Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily"
## [7] "Alcohol dehydrogenase GroES-like domain"
## [8] "K+ potassium transporter"
## [9] "Rieske [2Fe-2S] domain"
## [10] "ADP-ribosylation factor family"
## [11] "U-box domain"
## [12] "Pheophorbide a oxygenase"
## [13] "Glycosyltransferase family 28 C-terminal domain"
## [14] "Alpha galactosidase A"write.table(data.frame(EnrPiHigh$go$id, EnrPiHigh$go$padj), file = "GeneOntologyPiHigh.txt", sep = "\t",
row.names = FALSE)2.4.3 AZD effect
#’ #### Extraction of the results from the DESeq analysis
res_AZD <- results(dds_T6,name = "AZD_AZD_vs_DMSO")
cutoffs_AZD <- abs(res_AZD$log2FoldChange) >= lfc & ! is.na(res_AZD$padj) & res_AZD$padj <= FDR
cutoff1_AZD <- res_AZD$log2FoldChange >= lfc & ! is.na(res_AZD$padj) & res_AZD$padj <= FDR
cutoff2_AZD <- res_AZD$log2FoldChange <= -lfc & ! is.na(res_AZD$padj) & res_AZD$padj <= FDR
AZDEffect <- rownames(res_AZD[cutoffs_AZD,])
AZDLow <- rownames(res_AZD[cutoff2_AZD,])
AZDHigh <- rownames(res_AZD[cutoff1_AZD,])
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs_AZD)))## There are 6470 genes that are differentially expressedmessage(sprintf("There are %s genes that are induced",sum(cutoff1_AZD)))## There are 2866 genes that are inducedmessage(sprintf("There are %s genes that are repressed",sum(cutoff2_AZD)))## There are 3604 genes that are repressed2.4.3.0.1 MA plot
DESeq2::plotMA(res_AZD)
2.4.3.0.2 Volcano plot
volcanoPlot(res_AZD)
svg(filename="VolcanoAZD.svg",
width=10,
height=8,
pointsize=12)
volcanoPlot(res_AZD)
dev.off()## png
## 22.4.3.1 Enrichment analysis
2.4.3.1.1 Downregulated genes
EnrAZDLow <- gopher(AZDLow,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmanEnrAZDLow$go$name## [1] "non-membrane-bounded organelle"
## [2] "structural molecule activity"
## [3] "protein-containing complex"
## [4] "methylation"
## [5] "organelle part"
## [6] "cytosolic part"
## [7] "membrane-enclosed lumen"
## [8] "cellular component organization or biogenesis"
## [9] "cellular amide metabolic process"
## [10] "ribonucleoprotein complex"
## [11] "mitochondrial transport"
## [12] "cellular nitrogen compound metabolic process"
## [13] "ribonucleoprotein complex biogenesis"
## [14] "nitrogen compound metabolic process"
## [15] "protein alkylation"
## [16] "pyrimidine-containing compound metabolic process"
## [17] "cytosol"
## [18] "organelle"
## [19] "mitochondrion organization"
## [20] "protein localization to organelle"
## [21] "heterocycle metabolic process"
## [22] "organophosphate metabolic process"
## [23] "nuclear transport"
## [24] "RNA modification"
## [25] "peptidyl-amino acid modification"
## [26] "structural constituent of ribosome"
## [27] "protein localization to mitochondrion"
## [28] "multi-organism reproductive process"
## [29] "external encapsulating structure"
## [30] "DNA metabolic process"
## [31] "catalytic activity, acting on RNA"
## [32] "cell"
## [33] "cytoplasmic part"
## [34] "cellular process"
## [35] "macromolecule localization"
## [36] "organic cyclic compound metabolic process"
## [37] "symplast"
## [38] "envelope"
## [39] "cell junction"
## [40] "metabolic process"
## [41] "multicellular organism reproduction"
## [42] "cellular localization"
## [43] "cellular aromatic compound metabolic process"
## [44] "RNA binding"
## [45] "embryo sac development"
## [46] "ncRNA metabolic process"
## [47] "cellular response to DNA damage stimulus"
## [48] "macromolecule metabolic process"
## [49] "protein-containing complex localization"
## [50] "gene silencing"
## [51] "primary metabolic process"
## [52] "copper ion binding"
## [53] "gametophyte development"
## [54] "amide transport"
## [55] "cytoplasm"
## [56] "nucleotidyltransferase activity"
## [57] "heterocyclic compound binding"
## [58] "regulation of gene expression, epigenetic"
## [59] "cell proliferation"
## [60] "peptide metabolic process"
## [61] "nuclease activity"
## [62] "pyruvate metabolic process"
## [63] "ribonucleotide metabolic process"
## [64] "RNA processing"
## [65] "organic cyclic compound binding"
## [66] "gene expression"
## [67] "protein localization to nucleus"
## [68] "nucleobase-containing compound kinase activity"
## [69] "nuclear part"
## [70] "ribonucleoprotein complex localization"
## [71] "RNA localization"
## [72] "response to abiotic stimulus"
## [73] "response to cytokinin"
## [74] "biosynthetic process"
## [75] "intracellular"
## [76] "organelle organization"
## [77] "nucleobase-containing compound transport"
## [78] "cellular process involved in reproduction in multicellular organism"
## [79] "apoplast"
## [80] "reproduction"
## [81] "isopentenyl diphosphate metabolic process"
## [82] "organic substance transport"
## [83] "DNA replication"
## [84] "transferase activity, transferring one-carbon groups"
## [85] "cell cycle"
## [86] "protein transporter activity"
## [87] "whole membrane"
## [88] "negative regulation of metabolic process"
## [89] "catalytic activity, acting on DNA"
## [90] "nucleobase-containing small molecule metabolic process"
## [91] "isoprenoid metabolic process"
## [92] "DNA-dependent ATPase activity"
## [93] "hydrolase activity, acting on acid anhydrides"
## [94] "nucleoid"
## [95] "macromolecule transmembrane transporter activity"
## [96] "regulation of reproductive process"
## [97] "translation factor activity, RNA binding"
## [98] "response to metal ion"
## [99] "organic substance metabolic process"
## [100] "anatomical structure homeostasis"
## [101] "nucleobase-containing compound metabolic process"
## [102] "regulation of cell cycle"
## [103] "tubulin complex"
## [104] "amide transmembrane transporter activity"
## [105] "regulation of multicellular organismal process"
## [106] "helicase activity"
## [107] "response to carbohydrate"
## [108] "chromosome segregation"
## [109] "organelle fusion"
## [110] "regulation of developmental process"
## [111] "ligase activity"
## [112] "protein import"
## [113] "multicellular organismal process"
## [114] "ribosomal subunit"
## [115] "phosphotransferase activity, phosphate group as acceptor"
## [116] "female gamete generation"
## [117] "isomerase activity"
## [118] "response to ionizing radiation"
## [119] "ribose phosphate biosynthetic process"
## [120] "plant-type cell wall loosening"
## [121] "double-strand break repair"
## [122] "nitrogen compound transport"
## [123] "protein modification by small protein conjugation"
## [124] "protein deubiquitination"
## [125] "chromosome organization"
## [126] "lactate metabolic process"
## [127] "organonitrogen compound biosynthetic process"
## [128] "cell division"
## [129] "carbohydrate derivative metabolic process"
## [130] "organic substance biosynthetic process"
## [131] "reproductive system development"
## [132] "damaged DNA binding"
## [133] "single-stranded DNA binding"
## [134] "multidimensional cell growth"
## [135] "anatomical structure formation involved in morphogenesis"
## [136] "ribosome"
## [137] "carbohydrate derivative binding"
## [138] "cell cycle phase transition"
## [139] "organophosphate biosynthetic process"
## [140] "shoot system development"
## [141] "prosthetic group binding"
## [142] "plastid localization"
## [143] "double-stranded DNA binding"
## [144] "coenzyme metabolic process"
## [145] "nucleic acid transport"
## [146] "DNA-templated transcription, elongation"
## [147] "regulation of growth"
## [148] "negative regulation of gene expression, epigenetic"
## [149] "developmental process"
## [150] "mitochondrion"
## [151] "regulation of DNA metabolic process"
## [152] "maintenance of location"
## [153] "posttranscriptional regulation of gene expression"
## [154] "second-messenger-mediated signaling"
## [155] "protein folding"
## [156] "import into nucleus"
## [157] "plastid transcription"
## [158] "organonitrogen compound metabolic process"
## [159] "plastid"
## [160] "nucleoside phosphate biosynthetic process"
## [161] "photomorphogenesis"
## [162] "DNA secondary structure binding"
## [163] "multicellular organism development"
## [164] "ribosomal small subunit biogenesis"
## [165] "plastid stroma"
## [166] "oligosaccharyl transferase activity"
## [167] "phosphatidylglycerol metabolic process"
## [168] "superoxide metabolic process"
## [169] "cyclin-dependent protein kinase activity"
## [170] "plant-type ovary development"
## [171] "nucleus organization"
## [172] "response to salt stress"
## [173] "plant-type cell wall organization or biogenesis"
## [174] "nucleic acid phosphodiester bond hydrolysis"
## [175] "megagametogenesis"
## [176] "DNA conformation change"
## [177] "flower calyx development"
## [178] "omega-3 fatty acid desaturase activity"
## [179] "meristem development"
## [180] "cellular metabolic process"
## [181] "cell-cell signaling"
## [182] "response to red or far red light"
## [183] "regulation of nitrogen compound metabolic process"
## [184] "histone H3-K9 modification"
## [185] "glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity"
## [186] "cellular amino acid biosynthetic process"
## [187] "organelle assembly"
## [188] "cell differentiation"
## [189] "defense response to bacterium"
## [190] "protein-DNA complex subunit organization"
## [191] "regulation of biological process"
## [192] "post-embryonic plant morphogenesis"
## [193] "transferase complex"
## [194] "organophosphate ester transmembrane transporter activity"
## [195] "regulation of macromolecule metabolic process"
## [196] "amino acid activation"
## [197] "response to cadmium ion"
## [198] "succinate-CoA ligase activity"
## [199] "cellular metabolic compound salvage"
## [200] "RNA phosphodiester bond hydrolysis"
## [201] "response to misfolded protein"
## [202] "primary active transmembrane transporter activity"
## [203] "chloroplast organization"
## [204] "RNA phosphodiester bond hydrolysis, endonucleolytic"
## [205] "anion binding"
## [206] "protein localization to chloroplast"
## [207] "DNA replication initiation"
## [208] "negative regulation of biological process"
## [209] "tRNA metabolic process"
## [210] "pigment biosynthetic process"
## [211] "purine ribonucleoside triphosphate binding"
## [212] "ribonucleoprotein complex subunit organization"
## [213] "nucleoside metabolic process"
## [214] "cellular response to gravity"
## [215] "cellular response to auxin stimulus"
## [216] "lysine metabolic process"
## [217] "small molecule binding"
## [218] "replication fork"EnrAZDLow$kegg$id## [1] "3.6.4.13" "2.7.7.6" "3.6.5.3" "2.4.99.18" "2.1.1.125" "3.6.4.12"
## [7] "2.4.2.1" "1.2.1.12" "2.7.7.7" "3.1.26.5" "5.2.1.8" "5.3.4.1"EnrAZDLow$pfam$name## [1] "PPR repeat"
## [2] "PPR repeat family"
## [3] "Core histone H2A/H2B/H3/H4"
## [4] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [5] "TCP-1/cpn60 chaperonin family"
## [6] "LSM domain"
## [7] "Helicase conserved C-terminal domain"
## [8] "Elongation factor Tu GTP binding domain"
## [9] "60s Acidic ribosomal protein"
## [10] "Elongation factor Tu domain 2"
## [11] "50S ribosome-binding GTPase"
## [12] "MCM P-loop domain"
## [13] "Centromere kinetochore component CENP-T histone fold"
## [14] "Tubulin C-terminal domain"
## [15] "Tubulin/FtsZ family, GTPase domain"
## [16] "RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)"
## [17] "MCM N-terminal domain"
## [18] "DYW family of nucleic acid deaminases"
## [19] "Mitochondrial carrier protein"
## [20] "C-terminus of histone H2A"
## [21] "Mitochondrial glycoprotein"
## [22] "Ribosomal protein L13"
## [23] "Brix domain"
## [24] "Ribosomal protein L7/L12 C-terminal domain"
## [25] "3 exoribonuclease family, domain 1"
## [26] "Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A"
## [27] "Ribosomal protein L10"
## [28] "Transcription factor S-II (TFIIS)"
## [29] "Ribosomal protein L1p/L10e family"
## [30] "3 exoribonuclease family, domain 2"
## [31] "DEAD/DEAH box helicase"
## [32] "Ribosomal protein L11, N-terminal domain"
## [33] "Ribosomal protein L41"
## [34] "NAC domain"
## [35] "Ribosomal protein L30p/L7e"
## [36] "Ribosomal protein S5, C-terminal domain"
## [37] "Ribosomal protein S5, N-terminal domain"
## [38] "MutS domain I"
## [39] "KH domain"
## [40] "Ribosomal protein S10p/S20e"
## [41] "Ribosomal protein L5"
## [42] "ribosomal L5P family C-terminus"
## [43] "Type III restriction enzyme, res subunit"
## [44] "Ribosomal protein L11, RNA binding domain"
## [45] "S1 RNA binding domain"
## [46] "Zinc knuckle"
## [47] "KOW motif"
## [48] "OB-fold nucleic acid binding domain"
## [49] "WD domain, G-beta repeat"
## [50] "Elongation factor Tu C-terminal domain"
## [51] "16S rRNA methyltransferase RsmB/F"
## [52] "Phosphopantetheine attachment site"
## [53] "Pentatricopeptide repeat domain"
## [54] "Ribosomal protein L21e"
## [55] "Alba"
## [56] "Ribosomal protein S17"
## [57] "NOP5NT (NUC127) domain"
## [58] "FtsJ-like methyltransferase"
## [59] "N2,N2-dimethylguanosine tRNA methyltransferase"
## [60] "S25 ribosomal protein"
## [61] "Ribosomal protein L14p/L23e"
## [62] "GrpE"
## [63] "Importin-beta N-terminal domain"
## [64] "Eukaryotic translation initiation factor eIF2A"
## [65] "Nucleosome assembly protein (NAP)"
## [66] "Ribosomal L30 N-terminal domain"
## [67] "Domain of unknown function (DUF3523)"
## [68] "Histone-binding protein RBBP4 or subunit C of CAF1 complex"
## [69] "Ribosomal S17"
## [70] "Ribosomal protein L4/L1 family"
## [71] "MutS domain III"
## [72] "Ribosomal protein L19e"
## [73] "Ribosomal protein L7/L12 dimerisation domain"
## [74] "Ribosomal protein L35Ae"
## [75] "Dip2/Utp12 Family"
## [76] "Tim10/DDP family zinc finger"
## [77] "Ribosomal L29 protein"
## [78] "RNA polymerases M/15 Kd subunit"
## [79] "MutS domain II"
## [80] "DEAD_2"
## [81] "MutS domain V"
## [82] "Elongation factor G C-terminus"
## [83] "Hsp70 protein"
## [84] "Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain"
## [85] "Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain"
## [86] "Elongation factor G, domain IV"
## [87] "Domain of unknown function (DUF4217)"
## [88] "Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD"
## [89] "Pollen allergen"
## [90] "Domain found in IF2B/IF5"
## [91] "Ribosomal protein L19"
## [92] "DNA polymerase family B, exonuclease domain"
## [93] "WPP domain"
## [94] "Tim17/Tim22/Tim23/Pmp24 family"
## [95] "DNA polymerase family B"
## [96] "Ribosomal protein S13/S18"
## [97] "CoA-ligase"
## [98] "Ribosomal protein S11"
## [99] "Helicase C-terminal domain"
## [100] "Ribosomal protein S15"
## [101] "Replication protein A OB domain"
## [102] "SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397"
## [103] "Ribosomal protein L6"
## [104] "Calreticulin family"
## [105] "Replication factor-A protein 1, N-terminal domain"
## [106] "Lyase"
## [107] "Ribosomal protein S9/S16"
## [108] "Cobalamin synthesis protein cobW C-terminal domain"
## [109] "Initiation factor eIF2 gamma, C terminal"
## [110] "mTERF"
## [111] "Mitochondrial ATP synthase g subunit"
## [112] "Ribosomal protein S30"
## [113] "Ribosomal protein S19e"
## [114] "Single-strand binding protein family"
## [115] "Fatty acid desaturase"
## [116] "Ribosomal L27e protein family"
## [117] "Ribosomal family S4e"
## [118] "Ribosomal protein S28e"
## [119] "DNA polymerase alpha/epsilon subunit B"
## [120] "Ribosomal_S17 N-terminal"
## [121] "Ribosomal protein L24e"
## [122] "Ribosomal L22e protein family"
## [123] "Ribosomal protein L34e"
## [124] "E2F/DP family winged-helix DNA-binding domain"
## [125] "Ribosomal protein L6, N-terminal domain"
## [126] "Eukaryotic porin"
## [127] "Rad9"
## [128] "Ribosomal protein L31e"
## [129] "DNA-directed RNA polymerase N-terminal"
## [130] "Ribosomal L28e protein family"
## [131] "Gar1/Naf1 RNA binding region"
## [132] "S4 domain"
## [133] "Tetrapyrrole (Corrin/Porphyrin) Methylases"
## [134] "Ribosomal protein S21"
## [135] "Plant specific eukaryotic initiation factor 4B"
## [136] "RS4NT (NUC023) domain"
## [137] "Ribosomal L39 protein"
## [138] "Ribosomal protein S26e"
## [139] "Plectin/S10 domain"
## [140] "CBF/Mak21 family"
## [141] "Ribosomal protein S7e"
## [142] "Ribosomal protein L36e"
## [143] "Cse1"
## [144] "Ribosomal protein S6"
## [145] "Ribosomal protein S27a"
## [146] "Ribosomal protein L37e"
## [147] "DNA-dependent RNA polymerase"
## [148] "40S ribosomal protein S4 C-terminus"
## [149] "Ribosomal protein L6e"
## [150] "Nucleolar GTP-binding protein 1 (NOG1)"
## [151] "OST-HTH Associated domain"
## [152] "Ribosomal protein S8e"
## [153] "Sas10/Utp3/C1D family"
## [154] "Lytic transglycolase"write.table(data.frame(EnrAZDLow$go$id, EnrAZDLow$go$padj), file = "GeneOntologyAZDLow.txt", sep = "\t",
row.names = FALSE)2.4.3.1.2 Upregulated genes
EnrAZDHigh <- gopher(AZDHigh,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: kegg## No enrichments found in task: mapmanEnrAZDHigh$go$name## [1] "response to stimulus"
## [2] "cell death"
## [3] "pigment catabolic process"
## [4] "benzene-containing compound metabolic process"
## [5] "catabolic process"
## [6] "immune system process"
## [7] "aging"
## [8] "cell communication"
## [9] "tetrapyrrole metabolic process"
## [10] "microbody"
## [11] "cofactor catabolic process"
## [12] "secondary metabolic process"
## [13] "peroxisome organization"
## [14] "lipid metabolic process"
## [15] "localization"
## [16] "protein localization to membrane"
## [17] "regulation of response to stimulus"
## [18] "protein targeting"
## [19] "catalytic activity"
## [20] "cell periphery"
## [21] "respiratory burst"
## [22] "flavonoid metabolic process"
## [23] "process utilizing autophagic mechanism"
## [24] "defense response"
## [25] "liposaccharide metabolic process"
## [26] "signaling"
## [27] "response to nitrogen compound"
## [28] "response to drug"
## [29] "membrane"
## [30] "organic acid metabolic process"
## [31] "response to unfolded protein"
## [32] "response to fungus"
## [33] "reactive oxygen species metabolic process"
## [34] "indole-containing compound metabolic process"
## [35] "response to biotic stimulus"
## [36] "multi-organism process"
## [37] "protein localization to vacuole"
## [38] "lipid modification"
## [39] "organonitrogen compound metabolic process"
## [40] "protein modification process"
## [41] "antibiotic metabolic process"
## [42] "phenol-containing compound metabolic process"
## [43] "organic hydroxy compound metabolic process"
## [44] "drug metabolic process"
## [45] "intracellular signal transduction"
## [46] "tethering complex"
## [47] "response to chemical"
## [48] "vacuole"
## [49] "defense response, incompatible interaction"
## [50] "carbohydrate derivative biosynthetic process"
## [51] "response to oxygen-containing compound"
## [52] "olefin metabolic process"
## [53] "small molecule biosynthetic process"
## [54] "organic acid catabolic process"
## [55] "drug catabolic process"
## [56] "response to acid chemical"
## [57] "cellular macromolecule metabolic process"
## [58] "response to ethylene"
## [59] "response to external stimulus"
## [60] "response to organic cyclic compound"
## [61] "nucleobase metabolic process"
## [62] "regulation of protein metabolic process"
## [63] "glucan catabolic process"
## [64] "organonitrogen compound catabolic process"
## [65] "postreplication repair"
## [66] "pollen development"
## [67] "glycosyl compound metabolic process"
## [68] "response to wounding"
## [69] "pigment metabolic process"
## [70] "cytoskeleton"
## [71] "phosphorylation"
## [72] "cellular component macromolecule biosynthetic process"
## [73] "monocarboxylic acid metabolic process"
## [74] "cytoplasm"
## [75] "regulation of biological quality"
## [76] "PSII associated light-harvesting complex II catabolic process"
## [77] "DNA binding"
## [78] "signal transduction by protein phosphorylation"
## [79] "calmodulin binding"
## [80] "glycoprotein metabolic process"
## [81] "detection of stimulus"
## [82] "nitrogen compound transport"
## [83] "fatty acid metabolic process"
## [84] "protein localization"
## [85] "oxidation-reduction process"
## [86] "regulation of hormone levels"
## [87] "regulation of immune system process"
## [88] "chlorophyll metabolic process"
## [89] "response to endogenous stimulus"
## [90] "membrane docking"
## [91] "late endosome"
## [92] "aromatic compound biosynthetic process"
## [93] "lipoprotein metabolic process"
## [94] "plastid part"
## [95] "hormone metabolic process"
## [96] "response to antibiotic"
## [97] "sequence-specific DNA binding"
## [98] "cellular carbohydrate catabolic process"
## [99] "animal organ development"
## [100] "aromatic amino acid family metabolic process"
## [101] "oxidoreductase activity, acting on single donors with incorporation of molecular oxygen"
## [102] "protein N-linked glycosylation"
## [103] "amine metabolic process"
## [104] "response to stress"
## [105] "fatty acid derivative metabolic process"
## [106] "ion binding"
## [107] "stomatal movement"
## [108] "transport"
## [109] "nitrogen cycle metabolic process"EnrAZDHigh$kegg$id## NULLEnrAZDHigh$pfam$name## [1] "Ubiquitin-like autophagy protein Apg12"
## [2] "U-box domain"
## [3] "POT family"
## [4] "TIR domain"
## [5] "Acyl-CoA dehydrogenase, middle domain"
## [6] "Calmodulin binding protein-like"
## [7] "CG-1 domain"
## [8] "C2 domain"
## [9] "FMN-dependent dehydrogenase"
## [10] "Protein phosphatase 2C"
## [11] "Alpha/beta hydrolase family"
## [12] "Exo70 exocyst complex subunit"
## [13] "AMP-binding enzyme"
## [14] "Protein tyrosine kinase"
## [15] "Aldehyde dehydrogenase family"
## [16] "CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B"
## [17] "Yippee zinc-binding/DNA-binding /Mis18, centromere assembly"write.table(data.frame(EnrAZDHigh$go$id, EnrAZDHigh$go$padj), file = "GeneOntologyAZDHigh.txt", sep = "\t",
row.names = FALSE)2.4.3.2 Heatmap
2.4.3.2.1 Z-score
hm <- heatmap.2(t(scale(t(vsd_T6[cutoffs_AZD,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
svg(filename="HeatMapAZD.svg",
width=10,
height=8,
pointsize=12)
hm <- heatmap.2(t(scale(t(vsd_T6[cutoffs_AZD,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
dev.off()## png
## 22.4.3.2.2 Heatmaps with Fold-change
2.4.3.2.2.1 Without NPS_DMSO, average of replicates, conditions ordered alphabetically
hmfc <- heatmap.2(fc_T6[cutoffs_AZD,],
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
col=hpal, margins = c(6,5),cexCol = 0.8)
2.4.3.2.2.2 Without NPS_DMSO, average of replicates, conditions ordered by dendrogram
hmfc <- heatmap.2(fc_T6[cutoffs_AZD,],
trace = "none",labRow = FALSE,
col=hpal, margins = c(6,5),cexCol = 0.8)
2.4.3.2.2.3 Like above but genes organized by Pearson correlation
hmfc <- heatmap.2(fc_T6[cutoffs_AZD,],
trace = "none",labRow = FALSE,
col=hpal, margins = c(6,5),cexCol = 0.8,
distfun = pearson.dist)
2.4.3.2.2.4 With NPS_DMSO, all replicates, conditions ordered by dendrogram
hmfc <- heatmap.2(fc2_T6[cutoffs_AZD,],
trace = "none",labRow = FALSE,
col=hpal, margins = c(6,5),
labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],cexCol = 0.8)
2.4.3.2.2.5 With NPS_DMSO, all replicates, conditions ordered according to the experimental design
hmfc <- heatmap.2(fc2_T6[cutoffs_AZD,],
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
col=hpal, margins = c(6,5),
labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],cexCol = 0.8)
2.4.3.3 Cluster analysis
tree <- cutree(as.hclust(hm$rowDendrogram),6)
c1 <- names(tree)[tree==1]
message(sprintf("There are %s genes in the cluster1",length(c1)))## There are 3125 genes in the cluster1heatmap.2(t(scale(t(vsd_T6[c1,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
svg(filename="HeatMapCl1.svg",
width=10,
height=8,
pointsize=12)
heatmap.2(t(scale(t(vsd_T6[c1,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
dev.off()## png
## 2cluster1 <- names(tree)[tree==1]
write.csv(cluster1,"cluster1.csv")
ggplot(melt(vsd_T6[cluster1,]),aes(x=Var2,y=value,group=Var2)) + geom_boxplot() +
theme(axis.text.x = element_text(angle=90)) +
scale_x_discrete(label=paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],element_blank()) +
scale_y_continuous("expression (VST)")## Warning in melt(vsd_T6[cluster1, ]): The melt generic in data.table has
## been passed a matrix and will attempt to redirect to the relevant reshape2
## method; please note that reshape2 is deprecated, and this redirection is now
## deprecated as well. To continue using melt methods from reshape2 while both
## libraries are attached, e.g. melt.list, you can prepend the namespace like
## reshape2::melt(vsd_T6[cluster1, ]). In the next version, this warning will
## become an error.
c2 <- names(tree)[tree==2]
message(sprintf("There are %s genes in the cluster2",length(c2)))## There are 329 genes in the cluster2heatmap.2(t(scale(t(vsd_T6[c2,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
c3 <- names(tree)[tree==3]
message(sprintf("There are %s genes in the cluster3",length(c3)))## There are 599 genes in the cluster3heatmap.2(t(scale(t(vsd_T6[c3,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
c4 <- names(tree)[tree==4]
message(sprintf("There are %s genes in the cluster4",length(c4)))## There are 1937 genes in the cluster4heatmap.2(t(scale(t(vsd_T6[c4,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
svg(filename="HeatMapCl4.svg",
width=10,
height=8,
pointsize=12)
heatmap.2(t(scale(t(vsd_T6[c4,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
dev.off()## png
## 2cluster4 <- names(tree)[tree==4]
write.csv(cluster4,"cluster4.csv")
ggplot(melt(vsd_T6[cluster4,]),aes(x=Var2,y=value,group=Var2)) + geom_boxplot() +
theme(axis.text.x = element_text(angle=90)) +
scale_x_discrete(label=paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],element_blank()) +
scale_y_continuous("expression (VST)")## Warning in melt(vsd_T6[cluster4, ]): The melt generic in data.table has
## been passed a matrix and will attempt to redirect to the relevant reshape2
## method; please note that reshape2 is deprecated, and this redirection is now
## deprecated as well. To continue using melt methods from reshape2 while both
## libraries are attached, e.g. melt.list, you can prepend the namespace like
## reshape2::melt(vsd_T6[cluster4, ]). In the next version, this warning will
## become an error.
c5 <- names(tree)[tree==5]
message(sprintf("There are %s genes in the cluster5",length(c5)))## There are 340 genes in the cluster5heatmap.2(t(scale(t(vsd_T6[c5,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
c6 <- names(tree)[tree==6]
message(sprintf("There are %s genes in the cluster6",length(c6)))## There are 140 genes in the cluster6heatmap.2(t(scale(t(vsd_T6[c6,]))),col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
2.4.4 Analysis of cluster composition
2.4.4.1 Enrichment
2.4.4.1.1 Enrichment for cluster1
cl1 <- gopher(cluster1,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmancl1$go$name## [1] "non-membrane-bounded organelle"
## [2] "structural molecule activity"
## [3] "methylation"
## [4] "protein-containing complex"
## [5] "cytosolic part"
## [6] "membrane-enclosed lumen"
## [7] "organelle part"
## [8] "cellular component organization or biogenesis"
## [9] "cellular amide metabolic process"
## [10] "ribonucleoprotein complex"
## [11] "cellular nitrogen compound metabolic process"
## [12] "nitrogen compound metabolic process"
## [13] "mitochondrial transport"
## [14] "ribonucleoprotein complex biogenesis"
## [15] "protein alkylation"
## [16] "pyrimidine-containing compound metabolic process"
## [17] "cytosol"
## [18] "organelle"
## [19] "protein localization to organelle"
## [20] "heterocycle metabolic process"
## [21] "cellular response to DNA damage stimulus"
## [22] "mitochondrion organization"
## [23] "nuclear transport"
## [24] "catalytic activity, acting on RNA"
## [25] "RNA modification"
## [26] "peptidyl-amino acid modification"
## [27] "structural constituent of ribosome"
## [28] "macromolecule localization"
## [29] "cellular localization"
## [30] "cellular aromatic compound metabolic process"
## [31] "metabolic process"
## [32] "organophosphate metabolic process"
## [33] "cellular process"
## [34] "organic cyclic compound metabolic process"
## [35] "macromolecule metabolic process"
## [36] "DNA metabolic process"
## [37] "multi-organism reproductive process"
## [38] "primary metabolic process"
## [39] "cell"
## [40] "protein-containing complex localization"
## [41] "protein localization to mitochondrion"
## [42] "external encapsulating structure"
## [43] "embryo sac development"
## [44] "amide transport"
## [45] "ncRNA metabolic process"
## [46] "RNA binding"
## [47] "gene silencing"
## [48] "multicellular organism reproduction"
## [49] "gene expression"
## [50] "cell proliferation"
## [51] "cytoplasmic part"
## [52] "symplast"
## [53] "heterocyclic compound binding"
## [54] "cell junction"
## [55] "nucleotidyltransferase activity"
## [56] "organic cyclic compound binding"
## [57] "nuclease activity"
## [58] "gametophyte development"
## [59] "peptide metabolic process"
## [60] "reproduction"
## [61] "intracellular"
## [62] "organic substance transport"
## [63] "regulation of gene expression, epigenetic"
## [64] "organelle organization"
## [65] "ribonucleotide metabolic process"
## [66] "RNA processing"
## [67] "ribonucleoprotein complex localization"
## [68] "RNA localization"
## [69] "nuclear part"
## [70] "protein localization to nucleus"
## [71] "organic substance metabolic process"
## [72] "cell cycle"
## [73] "nucleobase-containing compound kinase activity"
## [74] "envelope"
## [75] "biosynthetic process"
## [76] "copper ion binding"
## [77] "response to abiotic stimulus"
## [78] "nitrogen compound transport"
## [79] "cellular process involved in reproduction in multicellular organism"
## [80] "pyruvate metabolic process"
## [81] "catalytic activity, acting on DNA"
## [82] "anatomical structure homeostasis"
## [83] "nucleobase-containing compound transport"
## [84] "protein transporter activity"
## [85] "transferase activity, transferring one-carbon groups"
## [86] "nucleobase-containing compound metabolic process"
## [87] "nucleoid"
## [88] "isoprenoid metabolic process"
## [89] "helicase activity"
## [90] "cytoplasm"
## [91] "chromosome segregation"
## [92] "regulation of reproductive process"
## [93] "multicellular organismal process"
## [94] "chromosome organization"
## [95] "DNA replication"
## [96] "macromolecule transmembrane transporter activity"
## [97] "negative regulation of metabolic process"
## [98] "protein import"
## [99] "regulation of multicellular organismal process"
## [100] "female gamete generation"
## [101] "response to cytokinin"
## [102] "reproductive system development"
## [103] "isopentenyl diphosphate metabolic process"
## [104] "response to ionizing radiation"
## [105] "DNA-dependent ATPase activity"
## [106] "nucleobase-containing small molecule metabolic process"
## [107] "nucleic acid transport"
## [108] "response to metal ion"
## [109] "anatomical structure formation involved in morphogenesis"
## [110] "hydrolase activity, acting on acid anhydrides"
## [111] "regulation of developmental process"
## [112] "cell division"
## [113] "amide transmembrane transporter activity"
## [114] "tubulin complex"
## [115] "ligase activity"
## [116] "regulation of cell cycle"
## [117] "ribosomal subunit"
## [118] "transferase complex"
## [119] "translation factor activity, RNA binding"
## [120] "response to red or far red light"
## [121] "developmental process"
## [122] "organelle fusion"
## [123] "negative regulation of gene expression, epigenetic"
## [124] "protein modification by small protein conjugation"
## [125] "whole membrane"
## [126] "single-stranded DNA binding"
## [127] "plant-type cell wall loosening"
## [128] "damaged DNA binding"
## [129] "cellular metabolic process"
## [130] "DNA-templated transcription, elongation"
## [131] "phosphotransferase activity, phosphate group as acceptor"
## [132] "protein deubiquitination"
## [133] "regulation of biological process"
## [134] "double-stranded DNA binding"
## [135] "cell cycle phase transition"
## [136] "double-strand break repair"
## [137] "shoot system development"
## [138] "ribose phosphate biosynthetic process"
## [139] "ribosome"
## [140] "maintenance of location"
## [141] "megagametogenesis"
## [142] "lactate metabolic process"
## [143] "response to virus"
## [144] "organophosphate biosynthetic process"
## [145] "plant-type cell wall organization or biogenesis"
## [146] "carbohydrate derivative binding"
## [147] "oligosaccharyl transferase activity"
## [148] "response to carbohydrate"
## [149] "plastid transcription"
## [150] "photomorphogenesis"
## [151] "multicellular organism development"
## [152] "organic substance biosynthetic process"
## [153] "regulation of DNA metabolic process"
## [154] "posttranscriptional regulation of gene expression"
## [155] "DNA secondary structure binding"
## [156] "ribosomal small subunit biogenesis"
## [157] "post-embryonic plant morphogenesis"
## [158] "nucleic acid phosphodiester bond hydrolysis"
## [159] "import into nucleus"
## [160] "mitochondrion"
## [161] "hydrolase activity"
## [162] "anion binding"
## [163] "apoplast"
## [164] "flower calyx development"
## [165] "nucleoside phosphate biosynthetic process"
## [166] "protein-DNA complex subunit organization"
## [167] "organonitrogen compound biosynthetic process"
## [168] "multidimensional cell growth"
## [169] "TIM23 mitochondrial import inner membrane translocase complex"
## [170] "amino acid activation"
## [171] "DNA conformation change"
## [172] "succinate-CoA ligase activity"
## [173] "negative regulation of biological process"
## [174] "nucleus organization"
## [175] "peptidyl-lysine modification"
## [176] "organelle assembly"
## [177] "regulation of growth"
## [178] "organophosphate ester transmembrane transporter activity"
## [179] "positive regulation of cellular process"
## [180] "RNA interference"
## [181] "histone H3-K9 modification"
## [182] "ribonucleoprotein complex subunit organization"
## [183] "response to mechanical stimulus"
## [184] "phosphatidylglycerol metabolic process"
## [185] "plastid localization"
## [186] "plant-type ovary development"
## [187] "anion transmembrane transporter activity"
## [188] "second-messenger-mediated signaling"
## [189] "cyclin-dependent protein kinase activity"
## [190] "cell differentiation"
## [191] "lysine metabolic process"
## [192] "regulation of nitrogen compound metabolic process"
## [193] "cell-cell signaling"
## [194] "omega-3 fatty acid desaturase activity"
## [195] "meristem development"
## [196] "isomerase activity"
## [197] "tRNA metabolic process"
## [198] "diaminopimelate metabolic process"
## [199] "cellular amino acid biosynthetic process"
## [200] "response to misfolded protein"
## [201] "binding"
## [202] "RNA phosphodiester bond hydrolysis"
## [203] "protein localization to chloroplast"
## [204] "negative regulation of molecular function"
## [205] "RNA phosphodiester bond hydrolysis, endonucleolytic"
## [206] "RNA splicing, via transesterification reactions"
## [207] "transcription coregulator activity"
## [208] "regulation of macromolecule metabolic process"
## [209] "anchored component of membrane"
## [210] "prosthetic group binding"
## [211] "carboxylic acid metabolic process"
## [212] "primary active transmembrane transporter activity"
## [213] "cellular response to gravity"
## [214] "monosaccharide metabolic process"
## [215] "regulation of cellular metabolic process"
## [216] "response to cadmium ion"
## [217] "organonitrogen compound metabolic process"
## [218] "replication fork"
## [219] "plastid stroma"
## [220] "superoxide metabolic process"
## [221] "DNA replication initiation"
## [222] "thioester metabolic process"
## [223] "sterol metabolic process"
## [224] "embryo development"
## [225] "organic cation transmembrane transporter activity"
## [226] "amidine-lyase activity"
## [227] "DNA modification"
## [228] "very long-chain fatty acid metabolic process"
## [229] "defense response to bacterium"cl1$kegg## # A tibble: 15 x 9
## def id m mt n name nt padj pval
## <chr> <chr> <int> <int> <int> <chr> <int> <dbl> <dbl>
## 1 https://www.kegg.… 3.6.4… 6834 101 771 KEGG Ter… 42 1.66e-12 3.99e-15
## 2 https://www.kegg.… 2.7.7… 6834 44 771 KEGG Ter… 22 4.13e- 8 1.99e-10
## 3 https://www.kegg.… 3.6.5… 6834 28 771 KEGG Ter… 16 6.76e- 7 4.88e- 9
## 4 https://www.kegg.… 3.6.4… 6834 88 771 KEGG Ter… 25 6.60e- 4 7.93e- 6
## 5 https://www.kegg.… 2.1.1… 6834 9 771 KEGG Ter… 7 6.60e- 4 6.65e- 6
## 6 https://www.kegg.… 2.7.7… 6834 30 771 KEGG Ter… 12 3.39e- 3 4.90e- 5
## 7 https://www.kegg.… 3.1.2… 6834 9 771 KEGG Ter… 6 7.48e- 3 1.26e- 4
## 8 https://www.kegg.… 2.4.2… 6834 11 771 KEGG Ter… 6 2.95e- 2 5.66e- 4
## 9 https://www.kegg.… 2.8.1… 6834 5 771 KEGG Ter… 4 3.13e- 2 7.32e- 4
## 10 https://www.kegg.… 2.1.1… 6834 55 771 KEGG Ter… 15 3.13e- 2 8.27e- 4
## 11 https://www.kegg.… 2.4.9… 6834 8 771 KEGG Ter… 5 3.13e- 2 7.54e- 4
## 12 https://www.kegg.… 3.1.1… 6834 12 771 KEGG Ter… 6 3.55e- 2 1.03e- 3
## 13 https://www.kegg.… 6.2.1… 6834 3 771 KEGG Ter… 3 3.97e- 2 1.43e- 3
## 14 https://www.kegg.… 1.14.… 6834 3 771 KEGG Ter… 3 3.97e- 2 1.43e- 3
## 15 https://www.kegg.… 2.1.1… 6834 3 771 KEGG Ter… 3 3.97e- 2 1.43e- 3cl1$pfam$name## [1] "PPR repeat"
## [2] "PPR repeat family"
## [3] "Core histone H2A/H2B/H3/H4"
## [4] "TCP-1/cpn60 chaperonin family"
## [5] "Helicase conserved C-terminal domain"
## [6] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [7] "LSM domain"
## [8] "60s Acidic ribosomal protein"
## [9] "Elongation factor Tu GTP binding domain"
## [10] "DYW family of nucleic acid deaminases"
## [11] "Elongation factor Tu domain 2"
## [12] "50S ribosome-binding GTPase"
## [13] "RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)"
## [14] "DEAD/DEAH box helicase"
## [15] "Tubulin C-terminal domain"
## [16] "Tubulin/FtsZ family, GTPase domain"
## [17] "C-terminus of histone H2A"
## [18] "3 exoribonuclease family, domain 1"
## [19] "Ribosomal protein L10"
## [20] "Ribosomal protein L7/L12 C-terminal domain"
## [21] "Transcription factor S-II (TFIIS)"
## [22] "Centromere kinetochore component CENP-T histone fold"
## [23] "Ribosomal protein L1p/L10e family"
## [24] "Brix domain"
## [25] "Ribosomal protein L13"
## [26] "3 exoribonuclease family, domain 2"
## [27] "Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A"
## [28] "Type III restriction enzyme, res subunit"
## [29] "WD domain, G-beta repeat"
## [30] "ribosomal L5P family C-terminus"
## [31] "NAC domain"
## [32] "Ribosomal protein L5"
## [33] "Ribosomal protein L30p/L7e"
## [34] "MCM N-terminal domain"
## [35] "Ribosomal protein L11, N-terminal domain"
## [36] "S1 RNA binding domain"
## [37] "Ribosomal protein L11, RNA binding domain"
## [38] "Pentatricopeptide repeat domain"
## [39] "KH domain"
## [40] "Ribosomal protein S5, N-terminal domain"
## [41] "MutS domain I"
## [42] "Ribosomal protein S5, C-terminal domain"
## [43] "Ribosomal protein L41"
## [44] "Mitochondrial glycoprotein"
## [45] "OB-fold nucleic acid binding domain"
## [46] "Zinc knuckle"
## [47] "MCM P-loop domain"
## [48] "16S rRNA methyltransferase RsmB/F"
## [49] "Elongation factor Tu C-terminal domain"
## [50] "Importin-beta N-terminal domain"
## [51] "Mitochondrial carrier protein"
## [52] "Nucleosome assembly protein (NAP)"
## [53] "Ribosomal protein L14p/L23e"
## [54] "MutS domain III"
## [55] "Ribosomal L29 protein"
## [56] "Ribosomal protein S17"
## [57] "Histone-binding protein RBBP4 or subunit C of CAF1 complex"
## [58] "Ribosomal L30 N-terminal domain"
## [59] "Eukaryotic translation initiation factor eIF2A"
## [60] "MutS domain II"
## [61] "DEAD_2"
## [62] "S25 ribosomal protein"
## [63] "Ribosomal protein L19e"
## [64] "GrpE"
## [65] "NOP5NT (NUC127) domain"
## [66] "Tim10/DDP family zinc finger"
## [67] "RNA polymerases M/15 Kd subunit"
## [68] "Dip2/Utp12 Family"
## [69] "N2,N2-dimethylguanosine tRNA methyltransferase"
## [70] "Ribosomal protein L7/L12 dimerisation domain"
## [71] "Ribosomal protein L4/L1 family"
## [72] "FtsJ-like methyltransferase"
## [73] "Ribosomal protein L21e"
## [74] "Domain of unknown function (DUF3523)"
## [75] "Ribosomal S17"
## [76] "MutS domain V"
## [77] "Domain of unknown function (DUF4217)"
## [78] "KOW motif"
## [79] "S4 domain"
## [80] "Replication protein A OB domain"
## [81] "Replication factor-A protein 1, N-terminal domain"
## [82] "Ribosomal protein L6"
## [83] "SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397"
## [84] "Lyase"
## [85] "CoA-ligase"
## [86] "Ribosomal protein S13/S18"
## [87] "Ribosomal protein L19"
## [88] "Ribosomal protein S11"
## [89] "Ribosomal protein S9/S16"
## [90] "DNA polymerase family B, exonuclease domain"
## [91] "Ribosomal protein S10p/S20e"
## [92] "Helicase C-terminal domain"
## [93] "DNA polymerase family B"
## [94] "WPP domain"
## [95] "Ribosomal protein S15"
## [96] "Domain found in IF2B/IF5"
## [97] "Ribosomal protein L6, N-terminal domain"
## [98] "Ribosomal protein L6e"
## [99] "Plectin/S10 domain"
## [100] "Ribosomal L28e protein family"
## [101] "Rad9"
## [102] "Eukaryotic porin"
## [103] "Ribosomal protein S26e"
## [104] "Mitochondrial ATP synthase g subunit"
## [105] "Plant specific eukaryotic initiation factor 4B"
## [106] "Ribosomal protein L24e"
## [107] "E2F/DP family winged-helix DNA-binding domain"
## [108] "Ribosomal_S17 N-terminal"
## [109] "Ribosomal protein S30"
## [110] "Ribosomal protein S27a"
## [111] "Gar1/Naf1 RNA binding region"
## [112] "Initiation factor eIF2 gamma, C terminal"
## [113] "Sas10/Utp3/C1D family"
## [114] "Ribosomal protein L34e"
## [115] "Ribosomal L39 protein"
## [116] "Cse1"
## [117] "Ribosomal protein L37e"
## [118] "Ribosomal protein S21"
## [119] "Ribosomal protein S8e"
## [120] "Ribosomal protein L31e"
## [121] "Nucleolar GTP-binding protein 1 (NOG1)"
## [122] "Cobalamin synthesis protein cobW C-terminal domain"
## [123] "Ribosomal L22e protein family"
## [124] "Ribosomal L27e protein family"
## [125] "Ribosomal protein S7e"
## [126] "DNA polymerase alpha/epsilon subunit B"
## [127] "Ribosomal protein S6"
## [128] "40S ribosomal protein S4 C-terminus"
## [129] "Ribosomal family S4e"
## [130] "RS4NT (NUC023) domain"
## [131] "CBF/Mak21 family"
## [132] "Ribosomal protein L36e"
## [133] "Ribosomal protein S19e"
## [134] "Ribosomal protein S28e"
## [135] "Single-strand binding protein family"
## [136] "DNA-dependent RNA polymerase"
## [137] "DNA-directed RNA polymerase N-terminal"
## [138] "Radical SAM superfamily"
## [139] "BRCA1 C Terminus (BRCT) domain"
## [140] "Elongation factor G C-terminus"
## [141] "SPFH domain / Band 7 family"
## [142] "Pollen allergen"
## [143] "snoRNA binding domain, fibrillarin"
## [144] "Adenylate kinase"
## [145] "Alba"write.csv(data.frame(cl1$go$id, cl1$go$padj),"GOofC1.csv")2.4.4.1.2 Enrichment for cluster4
cl4 <- gopher(cluster4,task=c("go","pfam","kegg"),background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: keggcl4$go$name## [1] "catabolic process"
## [2] "pigment catabolic process"
## [3] "peroxisome organization"
## [4] "response to stimulus"
## [5] "aging"
## [6] "process utilizing autophagic mechanism"
## [7] "cofactor catabolic process"
## [8] "lipid metabolic process"
## [9] "benzene-containing compound metabolic process"
## [10] "tetrapyrrole metabolic process"
## [11] "microbody"
## [12] "catalytic activity"
## [13] "liposaccharide metabolic process"
## [14] "organonitrogen compound metabolic process"
## [15] "cell death"
## [16] "secondary metabolic process"
## [17] "lipid modification"
## [18] "vesicle-mediated transport"
## [19] "protein localization to vacuole"
## [20] "protein targeting"
## [21] "vacuolar transport"
## [22] "cell communication"
## [23] "oxidation-reduction process"
## [24] "response to fungus"
## [25] "localization"
## [26] "cytoplasm"
## [27] "immune system process"
## [28] "regulation of response to stimulus"
## [29] "carbohydrate derivative biosynthetic process"
## [30] "fatty acid metabolic process"
## [31] "drug catabolic process"
## [32] "vacuole"
## [33] "flavonoid metabolic process"
## [34] "response to ethylene"
## [35] "glycoprotein metabolic process"
## [36] "drug metabolic process"
## [37] "reactive oxygen species metabolic process"
## [38] "cellular response to phosphate starvation"
## [39] "peroxisomal transport"
## [40] "pigment metabolic process"
## [41] "protein modification process"
## [42] "defense response, incompatible interaction"
## [43] "glycosylation"
## [44] "intracellular signal transduction"
## [45] "organic acid metabolic process"
## [46] "antibiotic metabolic process"
## [47] "phenol-containing compound metabolic process"
## [48] "monocarboxylic acid metabolic process"
## [49] "regulation of photosynthesis"
## [50] "postreplication repair"
## [51] "animal organ development"
## [52] "tethering complex"
## [53] "PSII associated light-harvesting complex II catabolic process"
## [54] "heat acclimation"
## [55] "pollen development"
## [56] "response to chemical"
## [57] "cellular component macromolecule biosynthetic process"
## [58] "organic acid catabolic process"
## [59] "response to symbiont"
## [60] "organelle membrane"
## [61] "nucleobase metabolic process"
## [62] "signaling"
## [63] "response to unfolded protein"
## [64] "organonitrogen compound catabolic process"
## [65] "protein localization"
## [66] "organic hydroxy compound metabolic process"
## [67] "signal transduction by protein phosphorylation"
## [68] "glucan catabolic process"
## [69] "glycine cleavage complex"
## [70] "ion binding"
## [71] "response to acid chemical"
## [72] "response to drug"cl4$kegg## NULLcl4$pfam$name## [1] "Ubiquitin-like autophagy protein Apg12"
## [2] "Acyl-CoA dehydrogenase, middle domain"
## [3] "Alpha/beta hydrolase family"
## [4] "CG-1 domain"
## [5] "Aldehyde dehydrogenase family"
## [6] "NAD binding domain of 6-phosphogluconate dehydrogenase"
## [7] "IPT/TIG domain"write.csv(data.frame(cl4$go$id, cl4$go$padj),"GOofC4.csv")2.4.5 Comparisons of GOI lists
2.4.5.1 Comparison of the DEGs in the different conditions
2.4.5.1.1 Venn diagram
# Require package VennDiagram
grid.draw(venn.diagram(list(AZDEffect, PiStarvEffect, SucStarvEffect),
filename=NULL,
col=pal[1:3],
category.names=c("AZD","Phos. Starv.","Suc. Starv.")))
2.4.5.2 Comparison of genes induced in the different conditions
grid.draw(venn.diagram(list(AZDHigh, PiStarvHigh, SucStarvHigh),
filename=NULL,
col=pal[1:3],
category.names=c("AZD+","Phos. Starv.+","Suc. Starv.+")))
2.4.5.2.1 GOI overlapping lists
UpOverlap <- intersect(AZDHigh,PiStarvHigh)
UpAzdSpecific <- setdiff(AZDHigh,PiStarvHigh)
UpPiSpecific <- setdiff(PiStarvHigh,AZDHigh)2.4.5.2.2 GO enrichment analysis
message(sprintf("There are %s genes commonly induced",length(UpOverlap)))## There are 1515 genes commonly inducedEnrUpOverlap <- gopher(UpOverlap,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmanEnrUpOverlap$go$name## [1] "catabolic process"
## [2] "lipid metabolic process"
## [3] "response to stimulus"
## [4] "process utilizing autophagic mechanism"
## [5] "benzene-containing compound metabolic process"
## [6] "aging"
## [7] "pigment catabolic process"
## [8] "cell death"
## [9] "liposaccharide metabolic process"
## [10] "organonitrogen compound metabolic process"
## [11] "secondary metabolic process"
## [12] "cofactor catabolic process"
## [13] "tetrapyrrole metabolic process"
## [14] "peroxisome organization"
## [15] "microbody"
## [16] "catalytic activity"
## [17] "vesicle-mediated transport"
## [18] "cell communication"
## [19] "protein localization to vacuole"
## [20] "localization"
## [21] "regulation of response to stimulus"
## [22] "vacuolar transport"
## [23] "response to fungus"
## [24] "protein targeting"
## [25] "cytoplasm"
## [26] "lipid modification"
## [27] "immune system process"
## [28] "postreplication repair"
## [29] "response to acid chemical"
## [30] "vacuole"
## [31] "heat acclimation"
## [32] "monocarboxylic acid metabolic process"
## [33] "pollen development"
## [34] "antibiotic metabolic process"
## [35] "multi-organism process"
## [36] "flavonoid metabolic process"
## [37] "signaling"
## [38] "cellular lipid metabolic process"
## [39] "oxidation-reduction process"
## [40] "carbohydrate derivative biosynthetic process"
## [41] "organic hydroxy compound metabolic process"
## [42] "response to external stimulus"
## [43] "regulation of microtubule-based process"
## [44] "reactive oxygen species metabolic process"
## [45] "response to biotic stimulus"
## [46] "response to ethylene"
## [47] "phenol-containing compound metabolic process"
## [48] "drug metabolic process"
## [49] "defense response, incompatible interaction"
## [50] "drug catabolic process"
## [51] "response to chemical"
## [52] "cytoskeleton"
## [53] "membrane lipid metabolic process"
## [54] "glycosylation"
## [55] "regulation of hormone levels"
## [56] "protein modification process"
## [57] "glycoprotein metabolic process"
## [58] "organic acid metabolic process"
## [59] "nucleobase metabolic process"
## [60] "response to oxygen-containing compound"
## [61] "erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process"
## [62] "intracellular signal transduction"
## [63] "lipoprotein metabolic process"
## [64] "signal transduction by protein phosphorylation"
## [65] "fatty acid metabolic process"
## [66] "response to stress"
## [67] "fatty acid derivative metabolic process"
## [68] "ubiquitin-like protein transferase activity"
## [69] "response to symbiont"
## [70] "cellular component macromolecule biosynthetic process"
## [71] "aromatic amino acid family metabolic process"
## [72] "ion binding"
## [73] "organic hydroxy compound catabolic process"EnrUpOverlap$kegg$id## [1] "1.6.5.5"EnrUpOverlap$pfam$name## [1] "Ubiquitin-like autophagy protein Apg12"
## [2] "NAD binding domain of 6-phosphogluconate dehydrogenase"
## [3] "ADP-ribosylation factor family"
## [4] "CG-1 domain"
## [5] "Sucrose synthase"
## [6] "Breast carcinoma amplified sequence 3"
## [7] "4Fe-4S single cluster domain of Ferredoxin I"write.table(data.frame(EnrUpOverlap$go$id, EnrUpOverlap$go$padj), file = "GeneOntologyUpOverlap.txt", sep = "\t",
row.names = FALSE)
message(sprintf("There are %s genes specifically induced by AZD",length(UpAzdSpecific)))## There are 1351 genes specifically induced by AZDEnrUpAZD <- gopher(UpAzdSpecific,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmanEnrUpAZD$go$name## [1] "defense response"
## [2] "immune system process"
## [3] "cell periphery"
## [4] "response to stimulus"
## [5] "response to nitrogen compound"
## [6] "protein localization to membrane"
## [7] "cell death"
## [8] "respiratory burst"
## [9] "membrane"
## [10] "cell communication"
## [11] "response to drug"
## [12] "response to unfolded protein"
## [13] "tetrapyrrole metabolic process"
## [14] "pigment catabolic process"
## [15] "flavonoid metabolic process"
## [16] "microbody"
## [17] "organic acid metabolic process"
## [18] "phosphorylation"
## [19] "benzene-containing compound metabolic process"
## [20] "signaling"
## [21] "localization"
## [22] "nitrogen cycle metabolic process"
## [23] "biological regulation"
## [24] "indole-containing compound metabolic process"
## [25] "aging"
## [26] "olefin metabolic process"
## [27] "protein targeting"
## [28] "secondary metabolic process"
## [29] "regulation of response to stimulus"
## [30] "ion transport"
## [31] "peroxisome organization"
## [32] "cofactor catabolic process"
## [33] "oligopeptide transport"
## [34] "reactive nitrogen species metabolic process"
## [35] "regulation of response to stress"
## [36] "reactive oxygen species metabolic process"
## [37] "transferase activity, transferring phosphorus-containing groups"
## [38] "regulation of biological quality"
## [39] "glycosyl compound metabolic process"
## [40] "response to biotic stimulus"
## [41] "response to aluminum ion"
## [42] "catalytic activity"EnrUpAZD$kegg$id## [1] "2.7.11.1" "6.3.1.2"EnrUpAZD$pfam$name## [1] "TIR domain"
## [2] "NB-ARC domain"
## [3] "Protein tyrosine kinase"
## [4] "Leucine Rich Repeat"
## [5] "POT family"
## [6] "Calmodulin binding protein-like"
## [7] "UvrB/uvrC motif"
## [8] "Glutamine synthetase, catalytic domain"
## [9] "Acyl-CoA dehydrogenase, N-terminal domain"
## [10] "OPT oligopeptide transporter protein"
## [11] "Cytochrome P450"write.table(data.frame(EnrUpAZD$go$id, EnrUpAZD$go$padj), file = "GeneOntologyUpAZD.txt", sep = "\t",
row.names = FALSE)
message(sprintf("There are %s genes specifically induced by phosphate starvation",length(UpPiSpecific)))## There are 1658 genes specifically induced by phosphate starvationEnrUpPi <- gopher(UpPiSpecific,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmanEnrUpPi$go$name## [1] "endomembrane system"
## [2] "response to stimulus"
## [3] "endomembrane system organization"
## [4] "cell periphery"
## [5] "liposaccharide metabolic process"
## [6] "response to inorganic substance"
## [7] "nucleoside diphosphate metabolic process"
## [8] "membrane lipid metabolic process"
## [9] "membrane"
## [10] "cell communication"
## [11] "nucleoside monophosphate metabolic process"
## [12] "nucleoside triphosphate metabolic process"
## [13] "cellular response to phosphate starvation"
## [14] "purine-containing compound metabolic process"
## [15] "protein localization to vacuole"
## [16] "vacuole"
## [17] "response to osmotic stress"
## [18] "localization"
## [19] "cellular response to external stimulus"
## [20] "carbohydrate derivative metabolic process"
## [21] "catabolic process"
## [22] "small molecule metabolic process"
## [23] "vacuole organization"
## [24] "response to extracellular stimulus"
## [25] "cytoplasm"
## [26] "carbohydrate metabolic process"
## [27] "response to stress"
## [28] "transporter activity"
## [29] "lipid metabolic process"
## [30] "hydrolase activity, acting on ester bonds"
## [31] "fluid transport"
## [32] "pyridine-containing compound metabolic process"
## [33] "response to alcohol"
## [34] "response to temperature stimulus"
## [35] "small molecule biosynthetic process"
## [36] "response to acid chemical"
## [37] "ATPase activity, coupled to movement of substances"
## [38] "response to lipid"
## [39] "symplast"
## [40] "cell junction"
## [41] "acid phosphatase activity"
## [42] "carbohydrate derivative biosynthetic process"
## [43] "pyridine-containing compound biosynthetic process"
## [44] "extracellular region"
## [45] "plant epidermal cell differentiation"
## [46] "vacuolar transport"
## [47] "postreplication repair"
## [48] "DNA binding"
## [49] "phosphoric ester hydrolase activity"
## [50] "response to oxygen-containing compound"
## [51] "oligosaccharide biosynthetic process"
## [52] "drug metabolic process"
## [53] "flavonoid metabolic process"
## [54] "secondary metabolic process"
## [55] "response to external stimulus"
## [56] "aromatic compound biosynthetic process"
## [57] "nucleobase-containing small molecule biosynthetic process"
## [58] "cofactor biosynthetic process"
## [59] "heterocycle biosynthetic process"
## [60] "trehalose metabolic process"
## [61] "proteasome assembly"
## [62] "intramolecular transferase activity, phosphotransferases"
## [63] "sulfur compound metabolic process"
## [64] "ribonucleotide metabolic process"
## [65] "stomatal movement"
## [66] "anion homeostasis"
## [67] "vesicle"
## [68] "response to light stimulus"
## [69] "proteolysis"
## [70] "coenzyme metabolic process"
## [71] "organic cyclic compound biosynthetic process"EnrUpPi$kegg$id## [1] "3.1.3.2" "3.6.1.1" "3.1.4.1"EnrUpPi$pfam$name## [1] "Purple acid Phosphatase, N-terminal domain"
## [2] "Iron/zinc purple acid phosphatase-like protein C"
## [3] "Calcineurin-like phosphoesterase"
## [4] "K+ potassium transporter"
## [5] "Major Facilitator Superfamily"
## [6] "Glycerophosphoryl diester phosphodiesterase family"
## [7] "Putative Phosphatase"
## [8] "Late embryogenesis abundant (LEA) group 1"
## [9] "cAMP-regulated phosphoprotein/endosulfine conserved region"write.table(data.frame(EnrUpPi$go$id, EnrUpPi$go$padj), file = "GeneOntologyUpPi.txt", sep = "\t",
row.names = FALSE)2.4.5.3 Comparison of genes repressed in the different conditions
grid.draw(venn.diagram(list(AZDLow, PiStarvLow, SucStarvLow),
filename=NULL,
col=pal[1:3],
category.names=c("AZDlow","Phos. Starv.low","Suc. Starv.low")))
2.4.5.3.1 GOI overlapping lists
DownOverlap <- intersect(AZDLow,PiStarvLow)
DownAzdSpecific <- setdiff(AZDLow,PiStarvLow)
DownPiSpecific <- setdiff(PiStarvLow,AZDLow)2.4.5.3.2 GO enrichment analysis
message(sprintf("There are %s genes commonly repressed",length(DownOverlap)))## There are 2542 genes commonly repressedEnrDownOverlap <- gopher(DownOverlap,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmanEnrDownOverlap$go$name## [1] "non-membrane-bounded organelle"
## [2] "structural molecule activity"
## [3] "methylation"
## [4] "protein-containing complex"
## [5] "cytosolic part"
## [6] "membrane-enclosed lumen"
## [7] "organelle part"
## [8] "cellular component organization or biogenesis"
## [9] "ribonucleoprotein complex"
## [10] "cellular amide metabolic process"
## [11] "cellular nitrogen compound metabolic process"
## [12] "nitrogen compound metabolic process"
## [13] "protein alkylation"
## [14] "pyrimidine-containing compound metabolic process"
## [15] "ribonucleoprotein complex biogenesis"
## [16] "cytosol"
## [17] "mitochondrial transport"
## [18] "organelle"
## [19] "heterocycle metabolic process"
## [20] "protein localization to organelle"
## [21] "metabolic process"
## [22] "peptidyl-amino acid modification"
## [23] "RNA modification"
## [24] "cellular process"
## [25] "cellular response to DNA damage stimulus"
## [26] "structural constituent of ribosome"
## [27] "nuclear transport"
## [28] "cellular localization"
## [29] "macromolecule metabolic process"
## [30] "macromolecule localization"
## [31] "cellular aromatic compound metabolic process"
## [32] "organic cyclic compound metabolic process"
## [33] "primary metabolic process"
## [34] "DNA metabolic process"
## [35] "catalytic activity, acting on RNA"
## [36] "mitochondrion organization"
## [37] "protein-containing complex localization"
## [38] "organophosphate metabolic process"
## [39] "cell proliferation"
## [40] "multi-organism reproductive process"
## [41] "cell"
## [42] "heterocyclic compound binding"
## [43] "gene silencing"
## [44] "embryo sac development"
## [45] "organic cyclic compound binding"
## [46] "amide transport"
## [47] "gene expression"
## [48] "peptide metabolic process"
## [49] "gametophyte development"
## [50] "nucleotidyltransferase activity"
## [51] "ncRNA metabolic process"
## [52] "reproduction"
## [53] "external encapsulating structure"
## [54] "cytoplasmic part"
## [55] "organelle organization"
## [56] "organic substance transport"
## [57] "intracellular"
## [58] "regulation of gene expression, epigenetic"
## [59] "nuclease activity"
## [60] "ribonucleoprotein complex localization"
## [61] "protein localization to mitochondrion"
## [62] "RNA localization"
## [63] "RNA binding"
## [64] "multicellular organism reproduction"
## [65] "symplast"
## [66] "cell junction"
## [67] "cellular process involved in reproduction in multicellular organism"
## [68] "ribonucleotide metabolic process"
## [69] "catalytic activity, acting on DNA"
## [70] "protein localization to nucleus"
## [71] "cell cycle"
## [72] "RNA processing"
## [73] "nitrogen compound transport"
## [74] "chromosome organization"
## [75] "DNA replication"
## [76] "biosynthetic process"
## [77] "organic substance metabolic process"
## [78] "nuclear part"
## [79] "multicellular organismal process"
## [80] "hydrolase activity, acting on acid anhydrides"
## [81] "transferase activity, transferring one-carbon groups"
## [82] "isoprenoid metabolic process"
## [83] "anatomical structure homeostasis"
## [84] "negative regulation of metabolic process"
## [85] "nucleobase-containing compound metabolic process"
## [86] "envelope"
## [87] "protein transporter activity"
## [88] "nucleoid"
## [89] "nucleobase-containing compound transport"
## [90] "nucleobase-containing compound kinase activity"
## [91] "nucleic acid transport"
## [92] "protein import"
## [93] "DNA-dependent ATPase activity"
## [94] "regulation of reproductive process"
## [95] "isopentenyl diphosphate metabolic process"
## [96] "macromolecule transmembrane transporter activity"
## [97] "pyruvate metabolic process"
## [98] "regulation of biological process"
## [99] "copper ion binding"
## [100] "nucleobase-containing small molecule metabolic process"
## [101] "developmental process"
## [102] "response to cytokinin"
## [103] "shoot system development"
## [104] "chromosome segregation"
## [105] "female gamete generation"
## [106] "organelle fusion"
## [107] "helicase activity"
## [108] "cell division"
## [109] "response to ionizing radiation"
## [110] "regulation of multicellular organismal process"
## [111] "response to abiotic stimulus"
## [112] "anatomical structure formation involved in morphogenesis"
## [113] "ligase activity"
## [114] "protein modification by small protein conjugation"
## [115] "reproductive system development"
## [116] "post-embryonic plant morphogenesis"
## [117] "amide transmembrane transporter activity"
## [118] "single-stranded DNA binding"
## [119] "damaged DNA binding"
## [120] "response to red or far red light"
## [121] "regulation of cell cycle"
## [122] "cell cycle phase transition"
## [123] "apoplast"
## [124] "protein deubiquitination"
## [125] "double-stranded DNA binding"
## [126] "regulation of developmental process"
## [127] "response to virus"
## [128] "anion binding"
## [129] "regulation of DNA metabolic process"
## [130] "translation factor activity, RNA binding"
## [131] "plant-type cell wall organization or biogenesis"
## [132] "ribosomal subunit"
## [133] "double-strand break repair"
## [134] "organophosphate biosynthetic process"
## [135] "transferase complex"
## [136] "TIM23 mitochondrial import inner membrane translocase complex"
## [137] "multicellular organism development"
## [138] "protein-DNA complex subunit organization"
## [139] "ribosome"
## [140] "ribosomal small subunit biogenesis"
## [141] "negative regulation of gene expression, epigenetic"
## [142] "import into nucleus"
## [143] "tubulin complex"
## [144] "plastid"
## [145] "cellular metabolic process"
## [146] "response to carbohydrate"
## [147] "nucleus organization"
## [148] "posttranscriptional regulation of gene expression"
## [149] "plastid transcription"
## [150] "carbohydrate derivative binding"
## [151] "mitochondrion"
## [152] "organelle assembly"
## [153] "hydrolase activity"
## [154] "DNA secondary structure binding"
## [155] "whole membrane"
## [156] "anchored component of membrane"
## [157] "nucleic acid phosphodiester bond hydrolysis"
## [158] "RNA splicing, via transesterification reactions"
## [159] "ribonucleoprotein complex subunit organization"
## [160] "ribose phosphate biosynthetic process"
## [161] "histone H3-K9 modification"
## [162] "protein localization"
## [163] "binding"
## [164] "lactate metabolic process"
## [165] "cytoplasm"
## [166] "megagametogenesis"
## [167] "plastid localization"
## [168] "plant-type cell wall loosening"
## [169] "DNA conformation change"
## [170] "macromolecule modification"
## [171] "multidimensional cell growth"
## [172] "negative regulation of biological process"
## [173] "RNA phosphodiester bond hydrolysis"
## [174] "organic substance biosynthetic process"
## [175] "response to radiation"
## [176] "cell differentiation"
## [177] "phosphatidylglycerol metabolic process"
## [178] "response to metal ion"
## [179] "maintenance of location"
## [180] "peptidyl-lysine modification"
## [181] "anion transmembrane transporter activity"
## [182] "DNA modification"
## [183] "regulation of response to biotic stimulus"
## [184] "DNA-templated transcription, elongation"
## [185] "regulation of transferase activity"
## [186] "cyclin-dependent protein kinase activity"
## [187] "pseudouridine synthase activity"
## [188] "nucleoside metabolic process"
## [189] "DNA replication initiation"
## [190] "cell-cell signaling"
## [191] "regulation of growth"
## [192] "nucleoside phosphate biosynthetic process"
## [193] "omega-3 fatty acid desaturase activity"
## [194] "small molecule binding"
## [195] "isomerase activity"
## [196] "organonitrogen compound biosynthetic process"
## [197] "flower calyx development"
## [198] "positive regulation of cellular process"
## [199] "regulation of response to external stimulus"
## [200] "lysine metabolic process"
## [201] "phosphotransferase activity, phosphate group as acceptor"
## [202] "transferase activity, transferring pentosyl groups"
## [203] "plant-type ovary development"
## [204] "RNA phosphodiester bond hydrolysis, endonucleolytic"
## [205] "superoxide metabolic process"
## [206] "4-hydroxy-tetrahydrodipicolinate synthase"
## [207] "amino acid activation"
## [208] "prosthetic group binding"
## [209] "photomorphogenesis"
## [210] "chloroplast organization"
## [211] "establishment of localization in cell"
## [212] "regulation of macromolecule metabolic process"
## [213] "replication fork"
## [214] "monosaccharide metabolic process"
## [215] "response to mechanical stimulus"
## [216] "N-methyltransferase activity"
## [217] "immune effector process"
## [218] "plastid stroma"
## [219] "primary active transmembrane transporter activity"
## [220] "meristem development"
## [221] "protein localization to chloroplast"EnrDownOverlap$kegg$id## [1] "3.6.4.13" "3.6.5.3" "2.7.7.6" "3.6.4.12" "2.1.1.125"
## [6] "2.7.7.7" "2.8.1.6" "3.1.26.5" "1.14.13.39" "2.1.1.216"
## [11] "2.1.1.43" "2.4.2.1"EnrDownOverlap$pfam$name## [1] "PPR repeat"
## [2] "PPR repeat family"
## [3] "Core histone H2A/H2B/H3/H4"
## [4] "Helicase conserved C-terminal domain"
## [5] "TCP-1/cpn60 chaperonin family"
## [6] "Elongation factor Tu GTP binding domain"
## [7] "60s Acidic ribosomal protein"
## [8] "Elongation factor Tu domain 2"
## [9] "Ribosomal protein L7Ae/L30e/S12e/Gadd45 family"
## [10] "50S ribosome-binding GTPase"
## [11] "LSM domain"
## [12] "DYW family of nucleic acid deaminases"
## [13] "C-terminus of histone H2A"
## [14] "DEAD/DEAH box helicase"
## [15] "3 exoribonuclease family, domain 1"
## [16] "MCM P-loop domain"
## [17] "3 exoribonuclease family, domain 2"
## [18] "Ribosomal protein L1p/L10e family"
## [19] "Brix domain"
## [20] "Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A"
## [21] "Ribosomal protein L13"
## [22] "S1 RNA binding domain"
## [23] "Type III restriction enzyme, res subunit"
## [24] "MCM N-terminal domain"
## [25] "NAC domain"
## [26] "Ribosomal protein S5, N-terminal domain"
## [27] "Ribosomal protein S5, C-terminal domain"
## [28] "KH domain"
## [29] "Ribosomal protein L5"
## [30] "Ribosomal protein L30p/L7e"
## [31] "ribosomal L5P family C-terminus"
## [32] "Ribosomal protein L41"
## [33] "MutS domain I"
## [34] "Tubulin/FtsZ family, GTPase domain"
## [35] "Mitochondrial glycoprotein"
## [36] "Tubulin C-terminal domain"
## [37] "RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)"
## [38] "16S rRNA methyltransferase RsmB/F"
## [39] "Elongation factor Tu C-terminal domain"
## [40] "Centromere kinetochore component CENP-T histone fold"
## [41] "Pentatricopeptide repeat domain"
## [42] "Zinc knuckle"
## [43] "Nucleosome assembly protein (NAP)"
## [44] "MutS domain III"
## [45] "Ribosomal protein L14p/L23e"
## [46] "Ribosomal protein L10"
## [47] "Ribosomal L30 N-terminal domain"
## [48] "Ribosomal protein L19e"
## [49] "Dip2/Utp12 Family"
## [50] "N2,N2-dimethylguanosine tRNA methyltransferase"
## [51] "Domain of unknown function (DUF3523)"
## [52] "WD domain, G-beta repeat"
## [53] "S25 ribosomal protein"
## [54] "MutS domain V"
## [55] "NOP5NT (NUC127) domain"
## [56] "Tim10/DDP family zinc finger"
## [57] "MutS domain II"
## [58] "FtsJ-like methyltransferase"
## [59] "Ribosomal protein L21e"
## [60] "Ribosomal S17"
## [61] "OB-fold nucleic acid binding domain"
## [62] "Ribosomal protein L4/L1 family"
## [63] "DEAD_2"
## [64] "KOW motif"
## [65] "Importin-beta N-terminal domain"
## [66] "S4 domain"
## [67] "Helicase C-terminal domain"
## [68] "Ribosomal protein S10p/S20e"
## [69] "Ribosomal protein L11, RNA binding domain"
## [70] "Ribosomal protein S9/S16"
## [71] "Ribosomal protein L11, N-terminal domain"
## [72] "DNA polymerase family B"
## [73] "Ribosomal protein S11"
## [74] "Ribosomal protein L19"
## [75] "Domain found in IF2B/IF5"
## [76] "DNA polymerase family B, exonuclease domain"
## [77] "Replication protein A OB domain"
## [78] "Replication factor-A protein 1, N-terminal domain"
## [79] "E2F/DP family winged-helix DNA-binding domain"
## [80] "Gar1/Naf1 RNA binding region"
## [81] "Ribosomal protein L36e"
## [82] "Ribosomal protein L24e"
## [83] "Ribosomal protein L31e"
## [84] "Ribosomal protein L37e"
## [85] "Ribosomal protein S7e"
## [86] "Nucleolar GTP-binding protein 1 (NOG1)"
## [87] "Ribosomal protein L6e"
## [88] "Rad9"
## [89] "BRCA1 C Terminus (BRCT) domain"
## [90] "Elongation factor G C-terminus"
## [91] "DNA polymerase alpha/epsilon subunit B"
## [92] "Ribosomal L27e protein family"
## [93] "Ribosomal protein S26e"
## [94] "Ribosomal_S17 N-terminal"
## [95] "Ribosomal protein S6"
## [96] "40S ribosomal protein S4 C-terminus"
## [97] "Ribosomal protein S21"
## [98] "CBF/Mak21 family"
## [99] "Plectin/S10 domain"
## [100] "Ribosomal protein S27a"
## [101] "Single-strand binding protein family"
## [102] "Cse1"
## [103] "Ribosomal protein S19e"
## [104] "Ribosomal L39 protein"
## [105] "Ribosomal family S4e"
## [106] "Initiation factor eIF2 gamma, C terminal"
## [107] "DNA-dependent RNA polymerase"
## [108] "DNA-directed RNA polymerase N-terminal"
## [109] "Ribosomal protein S28e"
## [110] "Ribosomal protein S8e"
## [111] "Ribosomal protein S30"
## [112] "Ribosomal L22e protein family"
## [113] "Ribosomal protein L34e"
## [114] "Ribosomal protein L6, N-terminal domain"
## [115] "Ribosomal L28e protein family"
## [116] "RS4NT (NUC023) domain"
## [117] "Tim17/Tim22/Tim23/Pmp24 family"
## [118] "Ribosomal protein L7/L12 C-terminal domain"
## [119] "Ribosomal L29 protein"
## [120] "Ribosomal protein S17"
## [121] "Transcription factor S-II (TFIIS)"
## [122] "Alba"
## [123] "Histone-binding protein RBBP4 or subunit C of CAF1 complex"
## [124] "snoRNA binding domain, fibrillarin"
## [125] "mTERF"
## [126] "SET domain"
## [127] "Ribosomal protein S8"
## [128] "Elongation factor G, domain IV"
## [129] "tRNA synthetases class I (I, L, M and V)"
## [130] "tRNA pseudouridine synthase"
## [131] "Domain of unknown function (DUF4217)"
## [132] "Hsp90 protein"
## [133] "Ribosomal protein L35Ae"
## [134] "PRMT5 arginine-N-methyltransferase"
## [135] "Ribosomal protein L3"
## [136] "Ribosomal protein S4/S9 N-terminal domain"
## [137] "Mitochondrial carrier protein"
## [138] "Ribosomal protein S2"
## [139] "RNA polymerases M/15 Kd subunit"
## [140] "Prefoldin subunit"
## [141] "MutS family domain IV"
## [142] "Eukaryotic translation initiation factor eIF2A"
## [143] "Ribosomal protein S27"
## [144] "Replication factor C C-terminal domain"
## [145] "Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A"
## [146] "Ribosomal protein L23"
## [147] "PHD-like zinc-binding domain"
## [148] "Cold-shock DNA-binding domain"write.table(data.frame(EnrDownOverlap$go$id, EnrDownOverlap$go$padj), file = "GeneOntologyDownOverlap.txt", sep = "\t",
row.names = FALSE)
message(sprintf("There are %s genes specifically repressed by AZD",length(DownAzdSpecific)))## There are 1062 genes specifically repressed by AZDEnrDownAZD <- gopher(DownAzdSpecific,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmanEnrDownAZD$go$name## [1] "endomembrane system"
## [2] "cytoplasm"
## [3] "organelle part"
## [4] "cellular metabolic compound salvage"
## [5] "envelope"
## [6] "carbohydrate metabolic process"
## [7] "membrane"
## [8] "copper ion binding"
## [9] "response to endoplasmic reticulum stress"
## [10] "small molecule metabolic process"
## [11] "purine-containing compound metabolic process"
## [12] "carbohydrate derivative metabolic process"
## [13] "pyridine-containing compound metabolic process"
## [14] "nucleoside diphosphate metabolic process"
## [15] "intramolecular oxidoreductase activity"
## [16] "external encapsulating structure"
## [17] "organonitrogen compound metabolic process"
## [18] "symplast"
## [19] "nucleoside monophosphate metabolic process"
## [20] "proteasome assembly"
## [21] "mitochondrial transport"
## [22] "cell junction"
## [23] "protein localization to mitochondrion"
## [24] "nucleoside triphosphate metabolic process"
## [25] "cofactor metabolic process"
## [26] "cytoplasmic part"
## [27] "organophosphate metabolic process"
## [28] "pyruvate metabolic process"
## [29] "mitochondrion organization"
## [30] "cofactor biosynthetic process"
## [31] "coenzyme metabolic process"
## [32] "whole membrane"
## [33] "transferase activity, transferring glycosyl groups"
## [34] "response to abiotic stimulus"
## [35] "apoplast"
## [36] "fluid transport"
## [37] "catabolic process"
## [38] "protein folding"
## [39] "endoplasmic reticulum"
## [40] "multicellular organism reproduction"
## [41] "vacuole"
## [42] "response to metal ion"
## [43] "generation of precursor metabolites and energy"
## [44] "glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity"
## [45] "RNA binding"
## [46] "proteolysis"
## [47] "response to topologically incorrect protein"
## [48] "endomembrane system organization"
## [49] "response to inorganic substance"
## [50] "ribose phosphate metabolic process"
## [51] "sulfur compound metabolic process"EnrDownAZD$kegg$id## [1] "2.4.99.18" "5.3.4.1" "1.2.1.12" "3.6.1.1" "1.1.1.41"EnrDownAZD$pfam$name## [1] "Calreticulin family"
## [2] "Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain"
## [3] "Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain"
## [4] "Oxidoreductase NAD-binding domain"
## [5] "Thioredoxin-like domain"
## [6] "Mitochondrial carrier protein"write.table(data.frame(EnrDownAZD$go$id, EnrDownAZD$go$padj), file = "GeneOntologyDownAZD.txt", sep = "\t",
row.names = FALSE)
message(sprintf("There are %s genes specifically repressed by phosphate starvation",length(DownPiSpecific)))## There are 1279 genes specifically repressed by phosphate starvationEnrDownPi <- gopher(DownPiSpecific,background=rownames(vsd_T6)[rowSums(vsd_T6)>0],url="athaliana")## No enrichments found in task: mapmanEnrDownPi$go$name## [1] "cell cycle"
## [2] "cell division"
## [3] "microtubule-based process"
## [4] "cell proliferation"
## [5] "cellular component organization or biogenesis"
## [6] "flower calyx development"
## [7] "protein alkylation"
## [8] "post-embryonic plant morphogenesis"
## [9] "photosynthesis"
## [10] "corolla development"
## [11] "motor activity"
## [12] "shoot system development"
## [13] "heterocycle metabolic process"
## [14] "organic cyclic compound metabolic process"
## [15] "biological regulation"
## [16] "gene silencing"
## [17] "cellular aromatic compound metabolic process"
## [18] "thylakoid"
## [19] "organelle organization"
## [20] "nitrogen compound metabolic process"
## [21] "post-embryonic plant organ development"
## [22] "cytoskeleton organization"
## [23] "methylation"
## [24] "anatomical structure formation involved in morphogenesis"
## [25] "sulfur compound metabolic process"
## [26] "kinase regulator activity"
## [27] "ncRNA metabolic process"
## [28] "peptidyl-amino acid modification"
## [29] "response to blue light"
## [30] "plastid"
## [31] "isoprenoid metabolic process"
## [32] "mitotic cell cycle"
## [33] "anatomical structure morphogenesis"
## [34] "regulation of gene expression, epigenetic"
## [35] "NADP metabolic process"
## [36] "organelle localization"
## [37] "regulation of anatomical structure size"
## [38] "DNA metabolic process"
## [39] "adenylyl-sulfate reductase activity"
## [40] "glucose 6-phosphate metabolic process"
## [41] "plastid part"
## [42] "multicellular organismal process"
## [43] "sulfur compound transmembrane transporter activity"
## [44] "oligopeptide transport"
## [45] "reproduction"
## [46] "cell cycle phase transition"
## [47] "hydrolase activity, acting on acid anhydrides"
## [48] "sulfur compound transport"
## [49] "response to red light"
## [50] "NADPH dehydrogenase activity"
## [51] "binding"
## [52] "cytokinesis"
## [53] "serine family amino acid metabolic process"
## [54] "plastid organization"
## [55] "electron transport chain"
## [56] "response to red or far red light"
## [57] "macromolecule modification"
## [58] "cellular component organization"EnrDownPi$kegg$id## [1] "3.6.4.4" "3.6.4.5" "1.10.3.9" "1.8.99.2" "1.8.4.9"EnrDownPi$pfam$name## [1] "PPR repeat"
## [2] "PPR repeat family"
## [3] "Kinesin motor domain"
## [4] "DYW family of nucleic acid deaminases"
## [5] "Calponin homology (CH) domain"
## [6] "Cyclin, C-terminal domain"
## [7] "RING-like zinc finger"
## [8] "von Willebrand factor type A domain"
## [9] "PPR repeat"
## [10] "Protein of unknown function (DUF627)"
## [11] "Protein of unknown function (DUF629)"
## [12] "Cyclin, N-terminal domain"
## [13] "Pentatricopeptide repeat domain"
## [14] "Phosphoadenosine phosphosulfate reductase family"
## [15] "Mitochondrial function, CLU-N-term"
## [16] "(Dead): PF06548"
## [17] "Leucine rich repeat N-terminal domain"
## [18] "Translation initiation factor eIF3 subunit 135"
## [19] "VWA / Hh protein intein-like"
## [20] "Plant organelle RNA recognition domain"write.table(data.frame(EnrDownPi$go$id, EnrDownPi$go$padj), file = "GeneOntologyDownPi.txt", sep = "\t",
row.names = FALSE)2.4.6 Comparisons of treatments regarding the Cell cycle GO term
# Create list of important GO terms based on the GO terms enriched in the genes downregulated after Pi starvation
myList <- c("GO:0007049", "GO:0044770", "GO:0016458", "GO:0000278", "GO:0006720", "GO:0007017", "GO:0040029",
"GO:0022900", "GO:0008283", "GO:0051301")
myList <- c("GO:0007049","GO:0090066","GO:0055086","GO:0048522","GO:0048519","GO:0009259","GO:0051726","GO:0006553",
"GO:0044770","GO:0009825","GO:0006090","GO:0022900","GO:0007059","GO:0060249","GO:0051301","GO:0019637",
"GO:0007267","GO:0050789","GO:0007017","GO:0010608","GO:0040029","GO:0046471","GO:0046490","GO:0040008",
"GO:0008652","GO:0008610","GO:0016458","GO:0006720","GO:0051171")
AZDLow <- AZDLow
PiStarvLow <- PiStarvLow
# Create list of genes in each GO term
geneList <- gopher(myList, task="go", url="athaliana", endpoint="term-to-gene")
#AZD_CellCycle <- lapply(geneList, function(x){intersect(x, AZDLow)})
#Pi_CellCycle <- lapply(geneList, function(x){intersect(x, PiStarvLow)})
# Remove the GO term having one or less gene
geneList <- geneList[lapply(geneList,length)>2]
geneList## $`GO:0008610`
## [1] "AT2G26250" "AT2G38700" "AT2G43710" "AT3G23470" "AT3G23510" "AT3G23530"
## [7] "AT3G54320"
##
## $`GO:0008652`
## [1] "AT1G04640" "AT1G08550" "AT1G11870" "AT1G23740" "AT1G68530" "AT1G70310"
## [7] "AT1G74960" "AT2G02500" "AT2G18950" "AT2G20610" "AT2G20860" "AT2G21330"
## [13] "AT2G22330" "AT2G22990" "AT2G27680" "AT2G30870" "AT2G35500" "AT2G37250"
## [19] "AT2G43710" "AT2G43750" "AT3G04790" "AT3G04940" "AT3G10030" "AT3G14110"
## [25] "AT3G25860" "AT3G26900" "AT3G45140" "AT3G59060" "AT3G62030" "AT4G01050"
## [31] "AT4G01900" "AT4G02680" "AT4G04640" "AT4G15560" "AT4G23600" "AT4G30950"
## [37] "AT4G31500" "AT4G32980" "AT4G33010" "AT4G34980" "AT4G38970" "AT4G39030"
## [43] "AT5G09660" "AT5G13280" "AT5G21060" "AT5G42650" "AT5G60600" "AT5G61130"
## [49] "AT5G62790" "ATCG01070"
##
## $`GO:0040008`
## [1] "AT1G16060" "AT1G65380" "AT3G23050" "AT5G20730" "AT5G60410"
##
## $`GO:0051726`
## [1] "AT1G01370" "AT1G02970" "AT1G03780" "AT1G04020" "AT1G05440" "AT1G07270"
## [7] "AT1G07370" "AT1G09450" "AT1G10780" "AT1G14750" "AT1G15570" "AT1G16330"
## [13] "AT1G18040" "AT1G20590" "AT1G20610" "AT1G22270" "AT1G24590" "AT1G27630"
## [19] "AT1G34460" "AT1G35440" "AT1G44110" "AT1G44900" "AT1G47210" "AT1G47220"
## [25] "AT1G47230" "AT1G50240" "AT1G53140" "AT1G57820" "AT1G59540" "AT1G65470"
## [31] "AT1G67320" "AT1G67630" "AT1G68310" "AT1G69770" "AT1G70210" "AT1G73690"
## [37] "AT1G75150" "AT1G76310" "AT1G77390" "AT1G78650" "AT1G78770" "AT1G80370"
## [43] "AT2G01905" "AT2G07170" "AT2G07690" "AT2G16440" "AT2G17620" "AT2G18040"
## [49] "AT2G20580" "AT2G21800" "AT2G22010" "AT2G22490" "AT2G23080" "AT2G24490"
## [55] "AT2G26430" "AT2G26760" "AT2G27040" "AT2G27960" "AT2G29680" "AT2G31270"
## [61] "AT2G31320" "AT2G32590" "AT2G33560" "AT2G36010" "AT2G36200" "AT2G38620"
## [67] "AT2G40030" "AT2G40550" "AT2G44740" "AT2G45080" "AT2G45280" "AT3G02820"
## [73] "AT3G03130" "AT3G06030" "AT3G11520" "AT3G12280" "AT3G18524" "AT3G20150"
## [79] "AT3G21870" "AT3G23580" "AT3G23740" "AT3G23890" "AT3G24320" "AT3G24495"
## [85] "AT3G27060" "AT3G42660" "AT3G49250" "AT3G50000" "AT3G50070" "AT3G51280"
## [91] "AT3G60550" "AT3G63120" "AT4G02070" "AT4G02460" "AT4G03270" "AT4G04950"
## [97] "AT4G09140" "AT4G14150" "AT4G14220" "AT4G18470" "AT4G19560" "AT4G19600"
## [103] "AT4G21820" "AT4G26660" "AT4G29170" "AT4G34160" "AT4G35620" "AT4G37490"
## [109] "AT4G37630" "AT5G02110" "AT5G02520" "AT5G06150" "AT5G07450" "AT5G08020"
## [115] "AT5G09790" "AT5G10440" "AT5G11300" "AT5G13960" "AT5G20850" "AT5G22000"
## [121] "AT5G24330" "AT5G25380" "AT5G27620" "AT5G27680" "AT5G40840" "AT5G43080"
## [127] "AT5G43990" "AT5G45190" "AT5G46280" "AT5G48600" "AT5G48630" "AT5G48640"
## [133] "AT5G49010" "AT5G55820" "AT5G57590" "AT5G61460" "AT5G61650" "AT5G62410"
## [139] "AT5G63920" "AT5G63950" "AT5G65420" "AT5G67100" "AT5G67260" "AT5G67380"
##
## $`GO:0009825`
## [1] "AT1G01610" "AT1G03060" "AT1G04040" "AT1G04430" "AT1G04680" "AT1G05850"
## [7] "AT1G10670" "AT1G12090" "AT1G13180" "AT1G20090" "AT1G20330" "AT1G20340"
## [13] "AT1G23080" "AT1G28440" "AT1G31420" "AT1G49040" "AT1G58250" "AT1G68530"
## [19] "AT1G69490" "AT1G70370" "AT1G70940" "AT1G75500" "AT1G75680" "AT1G75750"
## [25] "AT1G75780" "AT1G75840" "AT1G77690" "AT1G80350" "AT2G01420" "AT2G02130"
## [31] "AT2G03680" "AT2G06850" "AT2G20190" "AT2G22230" "AT2G35110" "AT2G35620"
## [37] "AT2G38120" "AT2G39900" "AT3G16370" "AT3G18780" "AT3G19820" "AT3G23050"
## [43] "AT3G25500" "AT3G26520" "AT3G27000" "AT3G28860" "AT3G46550" "AT3G49670"
## [49] "AT3G54920" "AT4G01710" "AT4G02500" "AT4G03190" "AT4G12420" "AT4G16370"
## [55] "AT4G18710" "AT4G20270" "AT4G22010" "AT4G25570" "AT4G32410" "AT4G33000"
## [61] "AT4G34490" "AT4G38430" "AT4G39400" "AT5G01090" "AT5G05170" "AT5G05690"
## [67] "AT5G10480" "AT5G12250" "AT5G13140" "AT5G15580" "AT5G16000" "AT5G16390"
## [73] "AT5G17690" "AT5G19530" "AT5G25810" "AT5G28646" "AT5G35360" "AT5G49720"
## [79] "AT5G55540" "AT5G60920" "AT5G64330" "AT5G64340" "AT5G64740" "AT5G65700"
##
## $`GO:0048519`
## [1] "AT1G04050" "AT1G05470" "AT1G12430" "AT1G19100" "AT1G19850" "AT1G30330"
## [7] "AT1G48410" "AT1G52150" "AT1G52310" "AT1G60860" "AT1G62360" "AT1G70510"
## [13] "AT1G73590" "AT1G78430" "AT1G79420" "AT1G79820" "AT2G16640" "AT2G27230"
## [19] "AT2G33860" "AT2G44830" "AT2G47230" "AT3G06220" "AT3G07540" "AT3G13510"
## [25] "AT3G28730" "AT3G43920" "AT3G54080" "AT4G08150" "AT4G30520" "AT4G32551"
## [31] "AT4G36260" "AT4G37750" "AT5G02030" "AT5G03680" "AT5G13300" "AT5G25475"
## [37] "AT5G37020" "AT5G43810" "AT5G57130" "AT5G58930" "AT5G60690" "AT5G61480"
## [43] "AT5G62710" "AT5G63950" "AT5G64340" "AT5G67200"
##
## $`GO:0016458`
## [1] "AT1G01370" "AT1G03780" "AT1G05440" "AT1G08130" "AT1G09450" "AT1G34355"
## [7] "AT1G44110" "AT1G50240" "AT1G53140" "AT1G59540" "AT1G63470" "AT1G63640"
## [13] "AT1G67630" "AT1G69770" "AT1G72250" "AT1G78770" "AT2G01120" "AT2G07170"
## [19] "AT2G22610" "AT2G24490" "AT2G27040" "AT2G31270" "AT2G31650" "AT2G32590"
## [25] "AT2G36200" "AT2G42120" "AT3G02470" "AT3G06930" "AT3G14190" "AT3G20260"
## [31] "AT3G22780" "AT3G23890" "AT3G24495" "AT3G42660" "AT3G44050" "AT3G51290"
## [37] "AT3G56870" "AT4G11130" "AT4G20910" "AT4G22860" "AT4G26760" "AT4G30860"
## [43] "AT4G33400" "AT4G39630" "AT5G08020" "AT5G14620" "AT5G15380" "AT5G15510"
## [49] "AT5G37010" "AT5G46280" "AT5G48600" "AT5G49020" "AT5G49160" "AT5G55520"
## [55] "AT5G58130" "AT5G62410" "AT5G63110" "AT5G63960"
##
## $`GO:0010608`
## [1] "AT4G08980" "AT4G21320" "AT5G60810"
##
## $`GO:0007059`
## [1] "AT1G50270" "AT1G63990" "AT1G67420" "AT1G67690" "AT1G69630" "AT1G70510"
## [7] "AT1G72270" "AT1G79890" "AT2G03430" "AT2G27170" "AT2G32900" "AT2G42720"
## [13] "AT3G01410" "AT3G02680" "AT3G10270" "AT3G10690" "AT3G13170" "AT3G20475"
## [19] "AT3G23890" "AT3G47950" "AT3G48190" "AT3G48210" "AT3G54670" "AT3G58210"
## [25] "AT3G61340" "AT4G16440" "AT4G17380" "AT4G35520" "AT5G04110" "AT5G04130"
## [31] "AT5G07660" "AT5G08220" "AT5G08450" "AT5G12260" "AT5G15920" "AT5G18810"
## [37] "AT5G18950" "AT5G48600" "AT5G57880" "AT5G60110" "AT5G61460" "AT5G63920"
## [43] "AT5G65180"
##
## $`GO:0051301`
## [1] "AT1G01370" "AT1G10270" "AT1G13980" "AT1G17580" "AT1G47870" "AT1G48410"
## [7] "AT1G50030" "AT1G55180" "AT1G55350" "AT1G56350" "AT1G57820" "AT1G59760"
## [13] "AT1G66740" "AT1G69670" "AT1G71830" "AT1G78580" "AT1G80620" "AT2G01500"
## [19] "AT2G20000" "AT2G26890" "AT2G28350" "AT2G34710" "AT2G34780" "AT2G38280"
## [25] "AT2G38560" "AT2G41260" "AT2G43790" "AT2G44190" "AT2G44950" "AT2G45160"
## [31] "AT2G47420" "AT3G08850" "AT3G09840" "AT3G10220" "AT3G12400" "AT3G18730"
## [37] "AT3G21510" "AT3G24650" "AT3G27670" "AT3G49240" "AT3G49600" "AT3G51810"
## [43] "AT3G59420" "AT3G60630" "AT3G60830" "AT3G61140" "AT4G00150" "AT4G00310"
## [49] "AT4G01560" "AT4G02460" "AT4G02570" "AT4G03240" "AT4G11140" "AT4G15900"
## [55] "AT4G21100" "AT4G21800" "AT4G22970" "AT4G26740" "AT4G28520" "AT4G30080"
## [61] "AT4G31160" "AT4G32010" "AT4G32720" "AT4G32880" "AT5G09810" "AT5G13480"
## [67] "AT5G15540" "AT5G16750" "AT5G20490" "AT5G22130" "AT5G22370" "AT5G27540"
## [73] "AT5G38110" "AT5G40770" "AT5G46210" "AT5G60410" "AT5G62440"
##
## $`GO:0007267`
## [1] "AT1G01040" "AT1G02900" "AT1G10180" "AT1G13220" "AT1G14690" "AT1G15940"
## [7] "AT1G18450" "AT1G23145" "AT1G23147" "AT1G26540" "AT1G28270" "AT1G32490"
## [13] "AT1G34355" "AT1G35467" "AT1G48410" "AT1G52310" "AT1G54490" "AT1G59750"
## [19] "AT1G60625" "AT1G60815" "AT1G60860" "AT1G61563" "AT1G61566" "AT1G63020"
## [25] "AT1G63470" "AT1G63640" "AT1G67720" "AT1G72970" "AT1G77720" "AT1G79950"
## [31] "AT1G80070" "AT2G04660" "AT2G16390" "AT2G19020" "AT2G19030" "AT2G19040"
## [37] "AT2G19045" "AT2G20660" "AT2G22055" "AT2G25420" "AT2G27040" "AT2G28290"
## [43] "AT2G31320" "AT2G31970" "AT2G32835" "AT2G32890" "AT2G33130" "AT2G33775"
## [49] "AT2G34825" "AT2G39810" "AT2G41500" "AT2G47230" "AT3G03300" "AT3G04735"
## [55] "AT3G05490" "AT3G12550" "AT3G14980" "AT3G16570" "AT3G20010" "AT3G20550"
## [61] "AT3G23805" "AT3G24340" "AT3G25165" "AT3G25170" "AT3G28730" "AT3G29780"
## [67] "AT3G43920" "AT3G49250" "AT3G57300" "AT3G60740" "AT3G61670" "AT4G02020"
## [73] "AT4G02460" "AT4G02680" "AT4G11130" "AT4G11510" "AT4G11653" "AT4G12970"
## [79] "AT4G13075" "AT4G13950" "AT4G14010" "AT4G15800" "AT4G20910" "AT4G30130"
## [85] "AT4G30520" "AT4G32551" "AT5G02030" "AT5G02520" "AT5G07660" "AT5G13000"
## [91] "AT5G13960" "AT5G20320" "AT5G23880" "AT5G25475" "AT5G35930" "AT5G43810"
## [97] "AT5G63960" "AT5G67070"
##
## $`GO:0007017`
## [1] "AT1G04820" "AT1G20010" "AT1G23220" "AT1G50010" "AT1G64740" "AT2G07170"
## [7] "AT2G16960" "AT2G29550" "AT2G35630" "AT2G40730" "AT3G16120" "AT3G44200"
## [13] "AT3G57060" "AT3G60740" "AT4G15930" "AT4G27360" "AT4G38950" "AT5G12250"
## [19] "AT5G19780" "AT5G20110" "AT5G23860" "AT5G48120" "KATE"
##
## $`GO:0040029`
## [1] "AT1G21700" "AT1G54490" "AT1G73100" "AT1G77300" "AT2G24740" "AT2G28290"
## [7] "AT2G33290" "AT2G33610" "AT2G35160" "AT2G46020" "AT2G47620" "AT3G17590"
## [13] "AT4G13520" "AT4G16280" "AT4G24680" "AT5G04940"
##
## $`GO:0048522`
## [1] "AT1G01160" "AT1G13050" "AT1G17680" "AT1G32810" "AT1G48380" "AT1G65660"
## [7] "AT1G69600" "AT1G72050" "AT1G79880" "AT2G19930" "AT2G35550" "AT2G39090"
## [13] "AT2G41070" "AT2G43190" "AT2G44270" "AT3G07740" "AT3G15180" "AT3G26744"
## [19] "AT3G54610" "AT4G15090" "AT4G16440" "AT4G25540" "AT4G30870" "AT5G03070"
## [25] "AT5G06950" "AT5G06960" "AT5G14960" "AT5G18950" "AT5G19020" "AT5G24630"
## [31] "AT5G27750"length(geneList)## [1] 14lengths(geneList)## GO:0008610 GO:0008652 GO:0040008 GO:0051726 GO:0009825 GO:0048519 GO:0016458
## 7 50 5 144 84 46 58
## GO:0010608 GO:0007059 GO:0051301 GO:0007267 GO:0007017 GO:0040029 GO:0048522
## 3 43 77 98 23 16 31lapply(geneList, function(x){length(x)})## $`GO:0008610`
## [1] 7
##
## $`GO:0008652`
## [1] 50
##
## $`GO:0040008`
## [1] 5
##
## $`GO:0051726`
## [1] 144
##
## $`GO:0009825`
## [1] 84
##
## $`GO:0048519`
## [1] 46
##
## $`GO:0016458`
## [1] 58
##
## $`GO:0010608`
## [1] 3
##
## $`GO:0007059`
## [1] 43
##
## $`GO:0051301`
## [1] 77
##
## $`GO:0007267`
## [1] 98
##
## $`GO:0007017`
## [1] 23
##
## $`GO:0040029`
## [1] 16
##
## $`GO:0048522`
## [1] 31lapply(geneList, function(x){length(intersect(x,AZDLow))})## $`GO:0008610`
## [1] 0
##
## $`GO:0008652`
## [1] 10
##
## $`GO:0040008`
## [1] 0
##
## $`GO:0051726`
## [1] 70
##
## $`GO:0009825`
## [1] 20
##
## $`GO:0048519`
## [1] 6
##
## $`GO:0016458`
## [1] 28
##
## $`GO:0010608`
## [1] 0
##
## $`GO:0007059`
## [1] 16
##
## $`GO:0051301`
## [1] 28
##
## $`GO:0007267`
## [1] 17
##
## $`GO:0007017`
## [1] 10
##
## $`GO:0040029`
## [1] 2
##
## $`GO:0048522`
## [1] 5lapply(geneList, function(x){length(intersect(x,AZDHigh))})## $`GO:0008610`
## [1] 1
##
## $`GO:0008652`
## [1] 7
##
## $`GO:0040008`
## [1] 1
##
## $`GO:0051726`
## [1] 2
##
## $`GO:0009825`
## [1] 5
##
## $`GO:0048519`
## [1] 3
##
## $`GO:0016458`
## [1] 1
##
## $`GO:0010608`
## [1] 0
##
## $`GO:0007059`
## [1] 1
##
## $`GO:0051301`
## [1] 5
##
## $`GO:0007267`
## [1] 3
##
## $`GO:0007017`
## [1] 2
##
## $`GO:0040029`
## [1] 1
##
## $`GO:0048522`
## [1] 1lapply(geneList, function(x){
goi <- res_AZD[rownames(res_AZD) %in% x,]
volcanoPlot(goi)
goi2 <- t(scale(t(vsd_T6[rownames(res_AZD) %in% x,])))
goi2 <- na.omit(goi2)
hm <- heatmap.2(goi2,col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
})
## $`GO:0008610`
## $`GO:0008610`$rowInd
## [1] 6 5 7 4 3 1 2
##
## $`GO:0008610`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0008610`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0008610`$carpet
## AT3G23530 AT3G23510 AT3G54320 AT3G23470 AT2G43710 AT2G26250
## P11554_207 -0.580561 0.9656632 1.1901044 -0.315613036 -0.4636765 -0.8866897
## P11554_208 1.230705 1.1524073 1.3799930 -1.881889602 -0.5086719 -1.4315348
## P11554_209 1.403376 0.6564052 0.4652879 -0.556125726 -0.2811387 -1.1309443
## P11554_210 -0.580561 1.2335552 1.1296868 -0.626869921 -0.3402225 0.5031475
## P11554_211 -0.580561 0.2800088 0.0434840 0.183599628 -0.3512663 0.3400428
## P11554_212 -0.580561 0.4367527 0.2257048 -0.248753080 -0.2079475 -0.4081840
## P11554_213 1.291344 1.2260649 0.8889575 -0.113096342 -1.0621916 -1.3259379
## P11554_214 1.137249 -1.0482995 0.6062896 1.153112397 -0.6561333 -0.5897074
## P11554_215 -0.580561 -1.0482995 1.2179651 0.471798353 -1.0627460 -0.9193993
## P11554_216 -0.580561 1.0834797 0.0673518 -0.709432179 -0.9398894 1.1732508
## P11554_217 -0.580561 0.4161077 -0.5650026 -0.271451529 -1.1144308 1.5883458
## P11554_218 -0.580561 0.9359512 0.2461454 0.007900055 -0.7716109 1.3331808
## P11554_225 2.484620 -1.0482995 -1.4276605 0.626294980 1.2830845 -0.6790456
## P11554_226 -0.580561 -1.0482995 -1.5421456 2.239259437 1.6394191 -0.3573238
## P11554_227 -0.580561 -1.0482995 -1.0305536 -1.881889602 1.4285532 -0.1245257
## P11554_228 -0.580561 -1.0482995 -0.3064594 0.272805155 0.5715266 0.5514491
## P11554_229 -0.580561 -1.0482995 -0.9913437 0.956833548 1.5396093 1.0823843
## P11554_230 -0.580561 -1.0482995 -1.5978050 0.693517464 1.2977326 1.2814914
## AT2G38700
## P11554_207 -1.6965200
## P11554_208 -1.1350345
## P11554_209 -0.3852578
## P11554_210 0.4836060
## P11554_211 0.2823746
## P11554_212 0.7290290
## P11554_213 -1.2677703
## P11554_214 -0.6888453
## P11554_215 -0.7989239
## P11554_216 1.3006001
## P11554_217 1.1175669
## P11554_218 1.1974590
## P11554_225 0.0885533
## P11554_226 0.6985871
## P11554_227 0.5267786
## P11554_228 -1.7554589
## P11554_229 0.7953479
## P11554_230 0.5079081
##
## $`GO:0008610`$rowDendrogram
## 'dendrogram' with 2 branches and 7 members total, at height 1.153919
##
## $`GO:0008610`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0008610`$breaks
## [1] -2.48461954 -2.43492715 -2.38523476 -2.33554237 -2.28584998 -2.23615759
## [7] -2.18646520 -2.13677281 -2.08708041 -2.03738802 -1.98769563 -1.93800324
## [13] -1.88831085 -1.83861846 -1.78892607 -1.73923368 -1.68954129 -1.63984890
## [19] -1.59015651 -1.54046412 -1.49077172 -1.44107933 -1.39138694 -1.34169455
## [25] -1.29200216 -1.24230977 -1.19261738 -1.14292499 -1.09323260 -1.04354021
## [31] -0.99384782 -0.94415543 -0.89446303 -0.84477064 -0.79507825 -0.74538586
## [37] -0.69569347 -0.64600108 -0.59630869 -0.54661630 -0.49692391 -0.44723152
## [43] -0.39753913 -0.34784674 -0.29815434 -0.24846195 -0.19876956 -0.14907717
## [49] -0.09938478 -0.04969239 0.00000000 0.04969239 0.09938478 0.14907717
## [55] 0.19876956 0.24846195 0.29815434 0.34784674 0.39753913 0.44723152
## [61] 0.49692391 0.54661630 0.59630869 0.64600108 0.69569347 0.74538586
## [67] 0.79507825 0.84477064 0.89446303 0.94415543 0.99384782 1.04354021
## [73] 1.09323260 1.14292499 1.19261738 1.24230977 1.29200216 1.34169455
## [79] 1.39138694 1.44107933 1.49077172 1.54046412 1.59015651 1.63984890
## [85] 1.68954129 1.73923368 1.78892607 1.83861846 1.88831085 1.93800324
## [91] 1.98769563 2.03738802 2.08708041 2.13677281 2.18646520 2.23615759
## [97] 2.28584998 2.33554237 2.38523476 2.43492715 2.48461954
##
## $`GO:0008610`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0008610`$colorTable
## low high color
## 1 -2.48461954 -2.43492715 #0000FF
## 2 -2.43492715 -2.38523476 #0505FF
## 3 -2.38523476 -2.33554237 #0A0AFF
## 4 -2.33554237 -2.28584998 #0F0FFF
## 5 -2.28584998 -2.23615759 #1414FF
## 6 -2.23615759 -2.18646520 #1919FF
## 7 -2.18646520 -2.13677281 #1E1EFF
## 8 -2.13677281 -2.08708041 #2424FF
## 9 -2.08708041 -2.03738802 #2929FF
## 10 -2.03738802 -1.98769563 #2E2EFF
## 11 -1.98769563 -1.93800324 #3333FF
## 12 -1.93800324 -1.88831085 #3838FF
## 13 -1.88831085 -1.83861846 #3D3DFF
## 14 -1.83861846 -1.78892607 #4242FF
## 15 -1.78892607 -1.73923368 #4848FF
## 16 -1.73923368 -1.68954129 #4D4DFF
## 17 -1.68954129 -1.63984890 #5252FF
## 18 -1.63984890 -1.59015651 #5757FF
## 19 -1.59015651 -1.54046412 #5C5CFF
## 20 -1.54046412 -1.49077172 #6161FF
## 21 -1.49077172 -1.44107933 #6767FF
## 22 -1.44107933 -1.39138694 #6C6CFF
## 23 -1.39138694 -1.34169455 #7171FF
## 24 -1.34169455 -1.29200216 #7676FF
## 25 -1.29200216 -1.24230977 #7B7BFF
## 26 -1.24230977 -1.19261738 #8080FF
## 27 -1.19261738 -1.14292499 #8585FF
## 28 -1.14292499 -1.09323260 #8B8BFF
## 29 -1.09323260 -1.04354021 #9090FF
## 30 -1.04354021 -0.99384782 #9595FF
## 31 -0.99384782 -0.94415543 #9A9AFF
## 32 -0.94415543 -0.89446303 #9F9FFF
## 33 -0.89446303 -0.84477064 #A4A4FF
## 34 -0.84477064 -0.79507825 #AAAAFF
## 35 -0.79507825 -0.74538586 #AFAFFF
## 36 -0.74538586 -0.69569347 #B4B4FF
## 37 -0.69569347 -0.64600108 #B9B9FF
## 38 -0.64600108 -0.59630869 #BEBEFF
## 39 -0.59630869 -0.54661630 #C3C3FF
## 40 -0.54661630 -0.49692391 #C8C8FF
## 41 -0.49692391 -0.44723152 #CECEFF
## 42 -0.44723152 -0.39753913 #D3D3FF
## 43 -0.39753913 -0.34784674 #D8D8FF
## 44 -0.34784674 -0.29815434 #DDDDFF
## 45 -0.29815434 -0.24846195 #E2E2FF
## 46 -0.24846195 -0.19876956 #E7E7FF
## 47 -0.19876956 -0.14907717 #ECECFF
## 48 -0.14907717 -0.09938478 #F2F2FF
## 49 -0.09938478 -0.04969239 #F7F7FF
## 50 -0.04969239 0.00000000 #FCFCFF
## 51 0.00000000 0.04969239 #FFFCFC
## 52 0.04969239 0.09938478 #FFF7F7
## 53 0.09938478 0.14907717 #FFF2F2
## 54 0.14907717 0.19876956 #FFECEC
## 55 0.19876956 0.24846195 #FFE7E7
## 56 0.24846195 0.29815434 #FFE2E2
## 57 0.29815434 0.34784674 #FFDDDD
## 58 0.34784674 0.39753913 #FFD8D8
## 59 0.39753913 0.44723152 #FFD3D3
## 60 0.44723152 0.49692391 #FFCECE
## 61 0.49692391 0.54661630 #FFC8C8
## 62 0.54661630 0.59630869 #FFC3C3
## 63 0.59630869 0.64600108 #FFBEBE
## 64 0.64600108 0.69569347 #FFB9B9
## 65 0.69569347 0.74538586 #FFB4B4
## 66 0.74538586 0.79507825 #FFAFAF
## 67 0.79507825 0.84477064 #FFA9A9
## 68 0.84477064 0.89446303 #FFA4A4
## 69 0.89446303 0.94415543 #FF9F9F
## 70 0.94415543 0.99384782 #FF9A9A
## 71 0.99384782 1.04354021 #FF9595
## 72 1.04354021 1.09323260 #FF9090
## 73 1.09323260 1.14292499 #FF8B8B
## 74 1.14292499 1.19261738 #FF8585
## 75 1.19261738 1.24230977 #FF8080
## 76 1.24230977 1.29200216 #FF7B7B
## 77 1.29200216 1.34169455 #FF7676
## 78 1.34169455 1.39138694 #FF7171
## 79 1.39138694 1.44107933 #FF6C6C
## 80 1.44107933 1.49077172 #FF6767
## 81 1.49077172 1.54046412 #FF6161
## 82 1.54046412 1.59015651 #FF5C5C
## 83 1.59015651 1.63984890 #FF5757
## 84 1.63984890 1.68954129 #FF5252
## 85 1.68954129 1.73923368 #FF4D4D
## 86 1.73923368 1.78892607 #FF4848
## 87 1.78892607 1.83861846 #FF4242
## 88 1.83861846 1.88831085 #FF3D3D
## 89 1.88831085 1.93800324 #FF3838
## 90 1.93800324 1.98769563 #FF3333
## 91 1.98769563 2.03738802 #FF2E2E
## 92 2.03738802 2.08708041 #FF2929
## 93 2.08708041 2.13677281 #FF2424
## 94 2.13677281 2.18646520 #FF1E1E
## 95 2.18646520 2.23615759 #FF1919
## 96 2.23615759 2.28584998 #FF1414
## 97 2.28584998 2.33554237 #FF0F0F
## 98 2.33554237 2.38523476 #FF0A0A
## 99 2.38523476 2.43492715 #FF0505
## 100 2.43492715 2.48461954 #FF0000
##
## $`GO:0008610`$layout
## $`GO:0008610`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0008610`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0008610`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0008652`
## $`GO:0008652`$rowInd
## [1] 7 25 6 47 12 13 3 8 43 28 18 39 21 1 44 23 34 49 10 16 46 9 38 30 15
## [26] 11 45 20 35 4 19 29 31 41 24 5 36 48 33 32 2 40 37 42 14 22 27 26 17
##
## $`GO:0008652`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0008652`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0008652`$carpet
## AT1G74960 AT3G25860 AT1G70310 AT5G61130 AT2G21330
## P11554_207 0.69680077 0.65070346 0.71737202 0.54006245 0.50846136
## P11554_208 1.11361739 1.03823571 1.02807959 0.57802113 0.88971593
## P11554_209 0.50847843 0.68539537 1.54779155 0.66827943 1.63257010
## P11554_210 -1.05691438 -0.94527232 -0.08393869 -0.37181561 0.01063041
## P11554_211 -0.80783948 -0.31718330 -0.48871238 -0.49997556 0.39941787
## P11554_212 -0.66059767 0.20921555 -0.22559678 -0.76360426 0.36201018
## P11554_213 1.49305345 1.39491023 1.28152254 1.55232444 0.53192184
## P11554_214 1.43510677 1.38280805 1.11851247 1.64141825 0.87622094
## P11554_215 1.52882834 1.52893211 1.74363710 2.03470130 0.60453128
## P11554_216 -0.45377065 0.17984916 -0.37204034 0.08318727 0.61496769
## P11554_217 -0.64250596 -0.01821190 -0.09766538 0.09955149 0.50330516
## P11554_218 0.06799104 -0.22423953 0.02691345 0.05913967 0.68928641
## P11554_225 -1.03894297 -0.72400014 -1.37434189 -0.71916572 -1.19950164
## P11554_226 0.72874505 -0.03461094 -1.12618589 -0.81677969 -1.11066898
## P11554_227 0.38472863 -0.28315894 -1.02774731 -0.60537081 -0.96557786
## P11554_228 -1.43255505 -1.94106027 -1.07725420 -1.22977063 -1.82599859
## P11554_229 -0.85482935 -1.24112973 -0.70792941 -0.90468698 -0.84013972
## P11554_230 -1.00939437 -1.34118259 -0.88241644 -1.34551616 -1.68115238
## AT2G22330 AT1G11870 AT2G02500 AT5G13280 AT3G62030 AT2G37250
## P11554_207 0.3600030 1.40601935 1.1323139 0.97493471 0.9749867 0.7879539
## P11554_208 0.5818213 0.78427808 1.0416064 1.07558454 1.4939521 0.6786573
## P11554_209 0.5386437 1.43903487 1.1785170 1.06698378 1.4701032 0.7142714
## P11554_210 -1.1143749 -0.95771765 -0.8535415 -0.90307178 -0.4759532 -1.0854617
## P11554_211 -0.8906497 -0.76268302 -0.7676931 -0.92374666 -0.4829757 -1.3333650
## P11554_212 -0.8971723 -0.97085346 -0.5656003 -1.00335791 -0.6848754 -1.1980971
## P11554_213 1.4354207 1.16418585 0.9882174 1.48204626 0.9636385 1.4215207
## P11554_214 1.2830436 1.31872352 1.4880468 1.41953505 1.3198069 1.3304527
## P11554_215 0.9594543 1.10955459 1.8283809 1.59689792 1.6586409 1.5320460
## P11554_216 0.9697285 -1.36274671 -0.9448187 -0.72418759 -0.6029954 -1.0715356
## P11554_217 0.8131284 -0.26408731 -1.2103924 -0.72824365 -0.3140318 -1.1255299
## P11554_218 1.0316569 -0.76602811 -0.7323867 -0.88970090 -0.5578570 -0.9564210
## P11554_225 -1.0463746 -0.01533128 -0.6916669 -0.05968623 -0.6637228 0.4910710
## P11554_226 -1.6371387 0.49589622 -0.3018784 0.07392075 -0.2707769 0.6030424
## P11554_227 -1.4105369 -0.07670779 0.4206978 0.21745356 -0.4627143 0.5504086
## P11554_228 -0.2280579 -0.94337335 -0.8941547 -0.96108622 -1.1317419 -0.4761506
## P11554_229 -0.2976821 -1.36370140 -0.6282014 -0.75407431 -1.2380530 -0.2858994
## P11554_230 -0.4509133 -0.23446242 -0.4874459 -0.96020133 -0.9954311 -0.5769639
## AT4G34980 AT3G04790 AT1G04640 AT5G21060 AT3G10030 AT4G23600
## P11554_207 1.2181334 1.6777420 0.90786835 -0.1594711 -0.71425888 -0.4343297
## P11554_208 1.1930584 1.3714635 0.23339080 -0.5665495 0.85903837 -0.4343297
## P11554_209 1.7034661 1.2125191 1.22235861 -0.2610359 0.23105365 -0.4343297
## P11554_210 -0.4201094 -0.1253824 -1.87370847 -1.0812718 -0.90589716 -0.4343297
## P11554_211 -0.4457936 0.3022390 -1.30008954 -1.0660961 -1.09876032 -0.4343297
## P11554_212 -0.1661040 -0.5237954 -0.99067467 -0.9080492 0.01569525 -0.4343297
## P11554_213 0.8371157 0.8382797 0.65100201 0.5270152 0.95100533 -0.4343297
## P11554_214 0.6260566 1.7259446 0.09067948 -0.2155024 0.39489053 -0.4343297
## P11554_215 -0.3032921 0.5511589 0.62807426 0.6874499 -0.44056126 -0.4343297
## P11554_216 -0.7282259 -0.6387814 -0.81861174 -1.1821384 0.80707995 2.2348060
## P11554_217 -0.9509326 -0.7401881 -0.33703149 0.5911991 0.07524211 -0.4343297
## P11554_218 -1.0715469 -0.6211192 -0.31326534 -0.1657748 0.92538018 2.0500497
## P11554_225 0.6750200 -0.4411076 -1.19462127 1.3608780 1.10472088 -0.4343297
## P11554_226 0.7894891 -0.3382698 0.66969827 1.8679844 0.68451943 -0.4343297
## P11554_227 0.9230606 -0.6997736 1.19099921 1.8942168 1.37849539 2.2300905
## P11554_228 -1.1919215 -0.9099134 -0.98088372 -1.3299344 -1.57981945 -0.4343297
## P11554_229 -1.1738312 -1.2448690 0.99034915 -0.3012573 -2.12020655 -0.4343297
## P11554_230 -1.5136429 -1.3961471 1.22446611 0.3083378 -0.56761745 -0.4343297
## ATCG01070 AT2G20610 AT2G30870 AT5G60600 AT2G18950
## P11554_207 -0.7623640 -0.64076574 -1.075556853 -1.0764900 -0.64529778
## P11554_208 1.1657208 -0.54321057 -1.040397812 -0.7124701 -0.65250686
## P11554_209 -0.7623640 -0.49484692 -1.031316474 -0.4792496 -0.81434456
## P11554_210 -0.7623640 -0.13193129 -0.154565824 0.5881398 0.83118204
## P11554_211 -0.7623640 0.08570855 -0.247429788 0.3674721 0.45101957
## P11554_212 1.0774095 -0.10965085 -0.321037310 0.4553470 0.51610491
## P11554_213 -0.7623640 -1.09654604 -1.285499358 -1.9371438 -1.54646969
## P11554_214 1.0662372 -1.51825967 -1.149442952 -1.2479480 -1.42113118
## P11554_215 1.1129940 -2.08007776 -1.055372176 -2.0124164 -1.70604107
## P11554_216 -0.7623640 0.09473628 -0.015913955 0.3133818 -0.23647511
## P11554_217 -0.7623640 -0.04128825 -0.079282933 0.3178745 -0.04596798
## P11554_218 -0.7623640 -0.02777732 0.001325816 0.1943313 -0.14380873
## P11554_225 -0.7623640 0.55184100 1.011141714 0.9435786 0.44989776
## P11554_226 1.1353535 0.85113374 1.191916527 0.7738874 0.22368420
## P11554_227 1.8739498 0.75234543 1.118986319 0.7042711 0.29338218
## P11554_228 0.9543392 1.08977166 1.269369405 0.6238547 1.50815327
## P11554_229 -0.7623640 1.82236350 1.361618355 0.9179960 1.43211942
## P11554_230 -0.7623640 1.43645424 1.501457299 1.2655838 1.50649959
## AT4G33010 AT4G01900 AT2G27680 AT2G20860 AT5G42650
## P11554_207 -0.79751282 -1.13582978 -1.05348527 -1.2598737 -0.3248354
## P11554_208 -0.55673970 -0.89764884 -0.63893035 -1.4318249 -0.6562852
## P11554_209 -0.34023730 -1.09826156 -0.51812593 -0.5217087 -0.7652403
## P11554_210 0.63425542 0.38616160 0.97246226 0.6263184 1.3546674
## P11554_211 0.71857495 -0.04912305 0.23733509 0.4104294 1.2419813
## P11554_212 0.68320564 1.71141326 0.83558819 0.5004638 0.8012580
## P11554_213 -1.77797330 -1.33013075 -1.48396686 -0.8247876 -1.2747600
## P11554_214 -1.81969947 -1.37117729 -2.05906045 -1.3473488 -1.7616964
## P11554_215 -1.65581505 -1.32081032 -1.60251349 -1.7940327 -1.8022336
## P11554_216 -0.11953527 1.12370511 0.79175386 0.5527037 0.6024822
## P11554_217 -0.07237331 -0.27537111 0.03827616 -0.1222958 0.2625571
## P11554_218 -0.05646012 0.21069897 0.84596420 0.6417128 -0.1150398
## P11554_225 0.36514936 0.38214859 0.75119657 -0.1333130 0.5615251
## P11554_226 0.64998928 0.81455083 0.63715924 0.6122372 -0.2056755
## P11554_227 0.60285327 0.10235144 0.69247777 0.4552230 -0.3550316
## P11554_228 0.91733261 0.55308314 -0.20656444 0.6281641 1.5623037
## P11554_229 1.07808572 0.70509514 1.12240121 1.9005520 0.6922793
## P11554_230 1.54690007 1.48914463 0.63803226 1.1073808 0.1817440
## AT2G43750 AT4G30950 AT1G23740 AT2G43710 AT4G01050
## P11554_207 -1.04583775 0.003993676 -0.22584667 -0.4636765 -0.7528272
## P11554_208 -0.81505103 -0.198306546 -0.55302264 -0.5086719 -0.1255583
## P11554_209 -0.23704660 -0.077647458 -0.00216094 -0.2811387 0.2480305
## P11554_210 0.95950712 -0.912223420 0.69169184 -0.3402225 -0.4768122
## P11554_211 0.95652509 -0.876306994 -0.50878261 -0.3512663 -0.2537767
## P11554_212 1.66701094 -0.784227550 -0.39271632 -0.2079475 -0.2810845
## P11554_213 -1.62473798 -0.496312645 -1.33800064 -1.0621916 -1.3255333
## P11554_214 -1.30348568 -0.449952774 -1.35886878 -0.6561333 -1.1663286
## P11554_215 -1.62871998 -0.607986464 -1.36312418 -1.0627460 -1.4380530
## P11554_216 0.54483165 -1.052171022 -0.79588454 -0.9398894 -0.7259700
## P11554_217 0.36099767 -0.984969278 -0.87756101 -1.1144308 -0.6005254
## P11554_218 -0.03382125 -1.172971832 -0.38490285 -0.7716109 -0.4018680
## P11554_225 -0.49920678 1.583599296 1.50824081 1.2830845 1.3464571
## P11554_226 0.18939811 1.610741204 1.29409450 1.6394191 1.5615625
## P11554_227 -0.19240917 1.688899156 1.20014628 1.4285532 1.6975123
## P11554_228 0.53636255 0.799030603 1.23627606 0.5715266 0.5368156
## P11554_229 1.39624687 0.866912544 1.07235791 1.5396093 1.0549943
## P11554_230 0.76943623 1.059899504 0.79806379 1.2977326 1.1029648
## AT4G02680 AT4G39030 AT3G14110 AT1G68530 AT4G31500
## P11554_207 -1.3308708 -0.89323649 -0.6774154 -1.2773911296 -0.27559324
## P11554_208 -0.6491262 -1.32260405 -1.7286164 -1.1411272076 -0.97343011
## P11554_209 -0.4068994 -1.46265968 -1.4273470 -1.2175560391 -0.85951058
## P11554_210 -0.5736486 1.07827390 0.7073673 -0.2245136358 0.06207055
## P11554_211 0.3698936 0.75118372 0.2925928 -0.0008749247 0.05343234
## P11554_212 0.2498876 0.72985866 0.5915166 -0.0421397731 -0.27771953
## P11554_213 0.6474680 -0.52720613 0.9723533 -1.0223561293 -0.71752109
## P11554_214 0.3597557 -0.58190710 -0.1317693 -1.3009825678 -0.61225557
## P11554_215 1.1507537 -0.25206680 -0.4088195 -0.3481235187 -1.43547746
## P11554_216 1.0755470 1.61262712 1.0319928 1.0051780263 1.64053446
## P11554_217 2.0377186 1.50984047 0.9025211 0.8429466639 1.55301332
## P11554_218 0.8150792 1.45254155 1.5144154 0.8449938383 1.66466478
## P11554_225 -0.2395097 -0.78147541 -1.7858228 0.0059472215 -0.86797408
## P11554_226 -1.6982802 -0.85093363 -0.7230147 -0.3915162970 -0.73266993
## P11554_227 -1.6565144 -0.93370846 -0.2459403 -0.2131078070 -0.84922889
## P11554_228 -0.3695215 0.07697024 -0.4478915 1.7929434057 0.81266527
## P11554_229 -0.3498109 0.41326435 0.9831420 1.0179811837 0.97952584
## P11554_230 0.5680783 -0.01876226 0.5807355 1.6696986903 0.83547395
## AT5G62790 AT4G15560 AT4G04640 AT1G08550 AT4G38970
## P11554_207 -0.6341806 -0.5372412 0.87712894 -0.51005235 1.20992394
## P11554_208 -0.8956040 -0.2954352 0.50089512 0.09685860 0.39390680
## P11554_209 -0.8134503 -0.1309909 0.87571583 1.04007710 1.59567827
## P11554_210 0.9513698 0.7360750 0.08284325 -0.35482782 0.27481832
## P11554_211 0.7890277 0.8167837 1.10169814 1.46356155 1.19877665
## P11554_212 0.9388398 0.8128913 0.08041826 0.10030770 1.17591094
## P11554_213 -1.2865187 -1.8189039 -2.42759508 -2.34087516 -1.26141345
## P11554_214 -1.3363753 -1.8318845 -0.92414557 -0.11372175 -1.88615270
## P11554_215 -1.3204754 -1.0332935 -1.37321461 -1.86848018 -1.65299774
## P11554_216 0.7379067 1.1122793 0.34788113 -0.82836153 -0.07472965
## P11554_217 1.0654858 0.7927959 1.01573131 1.28428810 0.20605233
## P11554_218 1.4072824 1.5203153 1.76340808 0.50939019 -0.74251855
## P11554_225 -0.4972821 -0.6841027 -0.19076523 0.14701284 0.55307613
## P11554_226 -0.6914302 -0.4213188 -0.40188394 -0.47878028 -0.27887884
## P11554_227 -0.7776355 -0.6696989 -0.65886381 0.27839133 0.40243956
## P11554_228 0.1241927 -0.1996072 -0.67180641 1.11103580 -0.91255397
## P11554_229 1.2383740 1.0092049 0.06107027 -0.01423311 0.07284534
## P11554_230 1.0004733 0.8221313 -0.05851570 0.47840897 -0.27418336
## AT4G32980 AT5G09660 AT2G22990 AT3G04940 AT3G59060
## P11554_207 0.92004112 0.14099361 0.45580762 0.07594759 0.65245528
## P11554_208 0.12241376 0.52146515 1.48086563 0.70208586 1.10553240
## P11554_209 0.25246247 -0.02992938 1.00095585 0.08069749 1.76662647
## P11554_210 0.17272932 1.40067556 0.86015568 0.84365442 -0.49689535
## P11554_211 -1.24175669 0.97407161 0.61015030 0.70335111 -0.18689407
## P11554_212 -1.24175669 0.36814729 1.28177553 1.19272393 -0.38392141
## P11554_213 -1.24175669 -0.93239626 -0.22699956 -0.83527856 0.08510004
## P11554_214 1.34490530 -0.46643123 0.50806124 0.24122219 -1.05542925
## P11554_215 0.63448352 -0.34567168 -0.82860728 -0.88003542 -1.44127630
## P11554_216 0.07967647 0.45225300 0.60233570 0.92018863 0.21464713
## P11554_217 1.62712588 0.49740097 -0.09880529 0.89758721 1.37658954
## P11554_218 -0.01179248 1.47996101 1.08356161 1.45869939 1.42560635
## P11554_225 -1.24175669 -2.13488353 -1.45449941 -1.44990118 -1.84800145
## P11554_226 -1.24175669 -0.16070651 -1.23648952 -1.87342632 -0.51559588
## P11554_227 -1.24175669 -0.50242660 -1.48074015 -1.18385563 0.38725782
## P11554_228 0.47578814 -2.14102712 -1.24508912 -0.82869772 -0.28334116
## P11554_229 1.02138078 0.49650433 -0.49687459 -0.68550947 0.04422181
## P11554_230 0.81132589 0.38199979 -0.81556423 0.62054647 -0.84668194
## AT3G26900 AT2G35500
## P11554_207 0.54377085 -1.98778073
## P11554_208 1.17612531 1.33998972
## P11554_209 1.26586722 0.86188361
## P11554_210 1.66060792 0.43831689
## P11554_211 0.04427991 0.23046142
## P11554_212 0.17265105 0.50794480
## P11554_213 -0.18967186 -0.49588934
## P11554_214 -1.68374217 -0.74010512
## P11554_215 0.57390569 -0.97476811
## P11554_216 -0.97983882 -0.58030181
## P11554_217 1.35404666 0.59494191
## P11554_218 -0.84852306 0.05209774
## P11554_225 -1.19615291 -0.15017546
## P11554_226 -1.21844001 -0.52518758
## P11554_227 0.61693795 0.09284449
## P11554_228 -0.65097687 -1.42466087
## P11554_229 -0.70139765 2.22378459
## P11554_230 0.06055078 0.53660384
##
## $`GO:0008652`$rowDendrogram
## 'dendrogram' with 2 branches and 49 members total, at height 2.847438
##
## $`GO:0008652`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0008652`$breaks
## [1] -2.4275951 -2.3790432 -2.3304913 -2.2819394 -2.2333875 -2.1848356
## [7] -2.1362837 -2.0877318 -2.0391799 -1.9906280 -1.9420761 -1.8935242
## [13] -1.8449723 -1.7964204 -1.7478685 -1.6993166 -1.6507647 -1.6022128
## [19] -1.5536608 -1.5051089 -1.4565570 -1.4080051 -1.3594532 -1.3109013
## [25] -1.2623494 -1.2137975 -1.1652456 -1.1166937 -1.0681418 -1.0195899
## [31] -0.9710380 -0.9224861 -0.8739342 -0.8253823 -0.7768304 -0.7282785
## [37] -0.6797266 -0.6311747 -0.5826228 -0.5340709 -0.4855190 -0.4369671
## [43] -0.3884152 -0.3398633 -0.2913114 -0.2427595 -0.1942076 -0.1456557
## [49] -0.0971038 -0.0485519 0.0000000 0.0485519 0.0971038 0.1456557
## [55] 0.1942076 0.2427595 0.2913114 0.3398633 0.3884152 0.4369671
## [61] 0.4855190 0.5340709 0.5826228 0.6311747 0.6797266 0.7282785
## [67] 0.7768304 0.8253823 0.8739342 0.9224861 0.9710380 1.0195899
## [73] 1.0681418 1.1166937 1.1652456 1.2137975 1.2623494 1.3109013
## [79] 1.3594532 1.4080051 1.4565570 1.5051089 1.5536608 1.6022128
## [85] 1.6507647 1.6993166 1.7478685 1.7964204 1.8449723 1.8935242
## [91] 1.9420761 1.9906280 2.0391799 2.0877318 2.1362837 2.1848356
## [97] 2.2333875 2.2819394 2.3304913 2.3790432 2.4275951
##
## $`GO:0008652`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0008652`$colorTable
## low high color
## 1 -2.4275951 -2.3790432 #0000FF
## 2 -2.3790432 -2.3304913 #0505FF
## 3 -2.3304913 -2.2819394 #0A0AFF
## 4 -2.2819394 -2.2333875 #0F0FFF
## 5 -2.2333875 -2.1848356 #1414FF
## 6 -2.1848356 -2.1362837 #1919FF
## 7 -2.1362837 -2.0877318 #1E1EFF
## 8 -2.0877318 -2.0391799 #2424FF
## 9 -2.0391799 -1.9906280 #2929FF
## 10 -1.9906280 -1.9420761 #2E2EFF
## 11 -1.9420761 -1.8935242 #3333FF
## 12 -1.8935242 -1.8449723 #3838FF
## 13 -1.8449723 -1.7964204 #3D3DFF
## 14 -1.7964204 -1.7478685 #4242FF
## 15 -1.7478685 -1.6993166 #4848FF
## 16 -1.6993166 -1.6507647 #4D4DFF
## 17 -1.6507647 -1.6022128 #5252FF
## 18 -1.6022128 -1.5536608 #5757FF
## 19 -1.5536608 -1.5051089 #5C5CFF
## 20 -1.5051089 -1.4565570 #6161FF
## 21 -1.4565570 -1.4080051 #6767FF
## 22 -1.4080051 -1.3594532 #6C6CFF
## 23 -1.3594532 -1.3109013 #7171FF
## 24 -1.3109013 -1.2623494 #7676FF
## 25 -1.2623494 -1.2137975 #7B7BFF
## 26 -1.2137975 -1.1652456 #8080FF
## 27 -1.1652456 -1.1166937 #8585FF
## 28 -1.1166937 -1.0681418 #8B8BFF
## 29 -1.0681418 -1.0195899 #9090FF
## 30 -1.0195899 -0.9710380 #9595FF
## 31 -0.9710380 -0.9224861 #9A9AFF
## 32 -0.9224861 -0.8739342 #9F9FFF
## 33 -0.8739342 -0.8253823 #A4A4FF
## 34 -0.8253823 -0.7768304 #AAAAFF
## 35 -0.7768304 -0.7282785 #AFAFFF
## 36 -0.7282785 -0.6797266 #B4B4FF
## 37 -0.6797266 -0.6311747 #B9B9FF
## 38 -0.6311747 -0.5826228 #BEBEFF
## 39 -0.5826228 -0.5340709 #C3C3FF
## 40 -0.5340709 -0.4855190 #C8C8FF
## 41 -0.4855190 -0.4369671 #CECEFF
## 42 -0.4369671 -0.3884152 #D3D3FF
## 43 -0.3884152 -0.3398633 #D8D8FF
## 44 -0.3398633 -0.2913114 #DDDDFF
## 45 -0.2913114 -0.2427595 #E2E2FF
## 46 -0.2427595 -0.1942076 #E7E7FF
## 47 -0.1942076 -0.1456557 #ECECFF
## 48 -0.1456557 -0.0971038 #F2F2FF
## 49 -0.0971038 -0.0485519 #F7F7FF
## 50 -0.0485519 0.0000000 #FCFCFF
## 51 0.0000000 0.0485519 #FFFCFC
## 52 0.0485519 0.0971038 #FFF7F7
## 53 0.0971038 0.1456557 #FFF2F2
## 54 0.1456557 0.1942076 #FFECEC
## 55 0.1942076 0.2427595 #FFE7E7
## 56 0.2427595 0.2913114 #FFE2E2
## 57 0.2913114 0.3398633 #FFDDDD
## 58 0.3398633 0.3884152 #FFD8D8
## 59 0.3884152 0.4369671 #FFD3D3
## 60 0.4369671 0.4855190 #FFCECE
## 61 0.4855190 0.5340709 #FFC8C8
## 62 0.5340709 0.5826228 #FFC3C3
## 63 0.5826228 0.6311747 #FFBEBE
## 64 0.6311747 0.6797266 #FFB9B9
## 65 0.6797266 0.7282785 #FFB4B4
## 66 0.7282785 0.7768304 #FFAFAF
## 67 0.7768304 0.8253823 #FFA9A9
## 68 0.8253823 0.8739342 #FFA4A4
## 69 0.8739342 0.9224861 #FF9F9F
## 70 0.9224861 0.9710380 #FF9A9A
## 71 0.9710380 1.0195899 #FF9595
## 72 1.0195899 1.0681418 #FF9090
## 73 1.0681418 1.1166937 #FF8B8B
## 74 1.1166937 1.1652456 #FF8585
## 75 1.1652456 1.2137975 #FF8080
## 76 1.2137975 1.2623494 #FF7B7B
## 77 1.2623494 1.3109013 #FF7676
## 78 1.3109013 1.3594532 #FF7171
## 79 1.3594532 1.4080051 #FF6C6C
## 80 1.4080051 1.4565570 #FF6767
## 81 1.4565570 1.5051089 #FF6161
## 82 1.5051089 1.5536608 #FF5C5C
## 83 1.5536608 1.6022128 #FF5757
## 84 1.6022128 1.6507647 #FF5252
## 85 1.6507647 1.6993166 #FF4D4D
## 86 1.6993166 1.7478685 #FF4848
## 87 1.7478685 1.7964204 #FF4242
## 88 1.7964204 1.8449723 #FF3D3D
## 89 1.8449723 1.8935242 #FF3838
## 90 1.8935242 1.9420761 #FF3333
## 91 1.9420761 1.9906280 #FF2E2E
## 92 1.9906280 2.0391799 #FF2929
## 93 2.0391799 2.0877318 #FF2424
## 94 2.0877318 2.1362837 #FF1E1E
## 95 2.1362837 2.1848356 #FF1919
## 96 2.1848356 2.2333875 #FF1414
## 97 2.2333875 2.2819394 #FF0F0F
## 98 2.2819394 2.3304913 #FF0A0A
## 99 2.3304913 2.3790432 #FF0505
## 100 2.3790432 2.4275951 #FF0000
##
## $`GO:0008652`$layout
## $`GO:0008652`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0008652`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0008652`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0040008`
## $`GO:0040008`$rowInd
## [1] 1 2 4 3 5
##
## $`GO:0040008`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0040008`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0040008`$carpet
## AT1G16060 AT1G65380 AT5G20730 AT3G23050 AT5G60410
## P11554_207 0.003822716 0.1286015 -1.23251527 -0.6671507 -1.7224402
## P11554_208 -0.681791439 -0.6044078 -0.91320308 -0.4122325 -1.3380981
## P11554_209 -0.872819982 -0.8055421 -0.86931678 -0.5860213 -0.4263909
## P11554_210 0.273053955 0.3917698 0.81532453 0.5106285 0.3838773
## P11554_211 0.429203908 -0.4977982 0.72896261 0.6011115 -0.2377363
## P11554_212 0.681451374 -0.3305242 1.02846490 1.1684395 0.2671240
## P11554_213 1.096372826 -0.6027961 -1.57035566 -1.5226191 -1.0146178
## P11554_214 0.095011915 -0.8652510 -1.39699704 -1.0109060 -1.0815673
## P11554_215 0.200507596 -1.2925528 -1.70675448 -2.0454680 -0.3549440
## P11554_216 1.129851382 -0.7114102 0.43880780 -0.6420635 -0.7733691
## P11554_217 1.614525061 -1.1084503 0.59753997 -0.4475978 0.5214622
## P11554_218 0.467708173 -0.9836600 0.48625911 -0.4689222 -0.3605248
## P11554_225 0.184327505 1.4623565 0.01106885 0.4232849 0.1017572
## P11554_226 -1.949556256 1.5550114 0.11474269 0.6429209 0.4062798
## P11554_227 0.373249598 1.4998173 0.37750056 1.0390648 0.9106027
## P11554_228 0.167040071 1.4283198 0.93845786 0.9715217 1.5149320
## P11554_229 -2.123960003 0.3258997 0.78565164 1.4351375 1.4812144
## P11554_230 -1.087998399 1.0106167 1.36636178 1.0108719 1.7224388
##
## $`GO:0040008`$rowDendrogram
## 'dendrogram' with 2 branches and 5 members total, at height 0.810927
##
## $`GO:0040008`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0040008`$breaks
## [1] -2.1239600 -2.0814808 -2.0390016 -1.9965224 -1.9540432 -1.9115640
## [7] -1.8690848 -1.8266056 -1.7841264 -1.7416472 -1.6991680 -1.6566888
## [13] -1.6142096 -1.5717304 -1.5292512 -1.4867720 -1.4442928 -1.4018136
## [19] -1.3593344 -1.3168552 -1.2743760 -1.2318968 -1.1894176 -1.1469384
## [25] -1.1044592 -1.0619800 -1.0195008 -0.9770216 -0.9345424 -0.8920632
## [31] -0.8495840 -0.8071048 -0.7646256 -0.7221464 -0.6796672 -0.6371880
## [37] -0.5947088 -0.5522296 -0.5097504 -0.4672712 -0.4247920 -0.3823128
## [43] -0.3398336 -0.2973544 -0.2548752 -0.2123960 -0.1699168 -0.1274376
## [49] -0.0849584 -0.0424792 0.0000000 0.0424792 0.0849584 0.1274376
## [55] 0.1699168 0.2123960 0.2548752 0.2973544 0.3398336 0.3823128
## [61] 0.4247920 0.4672712 0.5097504 0.5522296 0.5947088 0.6371880
## [67] 0.6796672 0.7221464 0.7646256 0.8071048 0.8495840 0.8920632
## [73] 0.9345424 0.9770216 1.0195008 1.0619800 1.1044592 1.1469384
## [79] 1.1894176 1.2318968 1.2743760 1.3168552 1.3593344 1.4018136
## [85] 1.4442928 1.4867720 1.5292512 1.5717304 1.6142096 1.6566888
## [91] 1.6991680 1.7416472 1.7841264 1.8266056 1.8690848 1.9115640
## [97] 1.9540432 1.9965224 2.0390016 2.0814808 2.1239600
##
## $`GO:0040008`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0040008`$colorTable
## low high color
## 1 -2.1239600 -2.0814808 #0000FF
## 2 -2.0814808 -2.0390016 #0505FF
## 3 -2.0390016 -1.9965224 #0A0AFF
## 4 -1.9965224 -1.9540432 #0F0FFF
## 5 -1.9540432 -1.9115640 #1414FF
## 6 -1.9115640 -1.8690848 #1919FF
## 7 -1.8690848 -1.8266056 #1E1EFF
## 8 -1.8266056 -1.7841264 #2424FF
## 9 -1.7841264 -1.7416472 #2929FF
## 10 -1.7416472 -1.6991680 #2E2EFF
## 11 -1.6991680 -1.6566888 #3333FF
## 12 -1.6566888 -1.6142096 #3838FF
## 13 -1.6142096 -1.5717304 #3D3DFF
## 14 -1.5717304 -1.5292512 #4242FF
## 15 -1.5292512 -1.4867720 #4848FF
## 16 -1.4867720 -1.4442928 #4D4DFF
## 17 -1.4442928 -1.4018136 #5252FF
## 18 -1.4018136 -1.3593344 #5757FF
## 19 -1.3593344 -1.3168552 #5C5CFF
## 20 -1.3168552 -1.2743760 #6161FF
## 21 -1.2743760 -1.2318968 #6767FF
## 22 -1.2318968 -1.1894176 #6C6CFF
## 23 -1.1894176 -1.1469384 #7171FF
## 24 -1.1469384 -1.1044592 #7676FF
## 25 -1.1044592 -1.0619800 #7B7BFF
## 26 -1.0619800 -1.0195008 #8080FF
## 27 -1.0195008 -0.9770216 #8585FF
## 28 -0.9770216 -0.9345424 #8B8BFF
## 29 -0.9345424 -0.8920632 #9090FF
## 30 -0.8920632 -0.8495840 #9595FF
## 31 -0.8495840 -0.8071048 #9A9AFF
## 32 -0.8071048 -0.7646256 #9F9FFF
## 33 -0.7646256 -0.7221464 #A4A4FF
## 34 -0.7221464 -0.6796672 #AAAAFF
## 35 -0.6796672 -0.6371880 #AFAFFF
## 36 -0.6371880 -0.5947088 #B4B4FF
## 37 -0.5947088 -0.5522296 #B9B9FF
## 38 -0.5522296 -0.5097504 #BEBEFF
## 39 -0.5097504 -0.4672712 #C3C3FF
## 40 -0.4672712 -0.4247920 #C8C8FF
## 41 -0.4247920 -0.3823128 #CECEFF
## 42 -0.3823128 -0.3398336 #D3D3FF
## 43 -0.3398336 -0.2973544 #D8D8FF
## 44 -0.2973544 -0.2548752 #DDDDFF
## 45 -0.2548752 -0.2123960 #E2E2FF
## 46 -0.2123960 -0.1699168 #E7E7FF
## 47 -0.1699168 -0.1274376 #ECECFF
## 48 -0.1274376 -0.0849584 #F2F2FF
## 49 -0.0849584 -0.0424792 #F7F7FF
## 50 -0.0424792 0.0000000 #FCFCFF
## 51 0.0000000 0.0424792 #FFFCFC
## 52 0.0424792 0.0849584 #FFF7F7
## 53 0.0849584 0.1274376 #FFF2F2
## 54 0.1274376 0.1699168 #FFECEC
## 55 0.1699168 0.2123960 #FFE7E7
## 56 0.2123960 0.2548752 #FFE2E2
## 57 0.2548752 0.2973544 #FFDDDD
## 58 0.2973544 0.3398336 #FFD8D8
## 59 0.3398336 0.3823128 #FFD3D3
## 60 0.3823128 0.4247920 #FFCECE
## 61 0.4247920 0.4672712 #FFC8C8
## 62 0.4672712 0.5097504 #FFC3C3
## 63 0.5097504 0.5522296 #FFBEBE
## 64 0.5522296 0.5947088 #FFB9B9
## 65 0.5947088 0.6371880 #FFB4B4
## 66 0.6371880 0.6796672 #FFAFAF
## 67 0.6796672 0.7221464 #FFA9A9
## 68 0.7221464 0.7646256 #FFA4A4
## 69 0.7646256 0.8071048 #FF9F9F
## 70 0.8071048 0.8495840 #FF9A9A
## 71 0.8495840 0.8920632 #FF9595
## 72 0.8920632 0.9345424 #FF9090
## 73 0.9345424 0.9770216 #FF8B8B
## 74 0.9770216 1.0195008 #FF8585
## 75 1.0195008 1.0619800 #FF8080
## 76 1.0619800 1.1044592 #FF7B7B
## 77 1.1044592 1.1469384 #FF7676
## 78 1.1469384 1.1894176 #FF7171
## 79 1.1894176 1.2318968 #FF6C6C
## 80 1.2318968 1.2743760 #FF6767
## 81 1.2743760 1.3168552 #FF6161
## 82 1.3168552 1.3593344 #FF5C5C
## 83 1.3593344 1.4018136 #FF5757
## 84 1.4018136 1.4442928 #FF5252
## 85 1.4442928 1.4867720 #FF4D4D
## 86 1.4867720 1.5292512 #FF4848
## 87 1.5292512 1.5717304 #FF4242
## 88 1.5717304 1.6142096 #FF3D3D
## 89 1.6142096 1.6566888 #FF3838
## 90 1.6566888 1.6991680 #FF3333
## 91 1.6991680 1.7416472 #FF2E2E
## 92 1.7416472 1.7841264 #FF2929
## 93 1.7841264 1.8266056 #FF2424
## 94 1.8266056 1.8690848 #FF1E1E
## 95 1.8690848 1.9115640 #FF1919
## 96 1.9115640 1.9540432 #FF1414
## 97 1.9540432 1.9965224 #FF0F0F
## 98 1.9965224 2.0390016 #FF0A0A
## 99 2.0390016 2.0814808 #FF0505
## 100 2.0814808 2.1239600 #FF0000
##
## $`GO:0040008`$layout
## $`GO:0040008`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0040008`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0040008`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0051726`
## $`GO:0051726`$rowInd
## [1] 85 133 16 45 99 132 48 105 76 21 140 52 55 116 96 50 17 128
## [19] 46 10 77 124 33 88 109 95 89 103 66 92 32 86 67 23 35 75
## [37] 44 108 104 24 5 79 18 72 101 3 87 53 14 26 100 136 112 39
## [55] 111 30 139 127 58 131 98 121 57 78 31 37 34 51 110 56 7 122
## [73] 2 107 106 6 28 126 81 19 135 27 69 74 42 43 125 29 65 138
## [91] 4 20 83 61 38 120 134 1 91 102 13 49 15 68 115 129 90 80
## [109] 97 82 73 118 113 60 93 25 36 12 94 64 11 54 119 8 70 9
## [127] 117 22 137 130 84 71 123 114 63 47 40 41 62 59
##
## $`GO:0051726`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0051726`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0051726`$carpet
## AT3G50000 AT5G61650 AT1G27630 AT2G18040 AT4G19600
## P11554_207 -1.16018750 -0.6762369 0.14747698 -0.27516193 -0.25477782
## P11554_208 -0.41095023 -0.6762369 0.39073518 0.04484604 -0.24066306
## P11554_209 0.20451150 -0.6762369 0.31208327 0.25475345 -0.46251849
## P11554_210 -1.44683019 -0.6762369 -0.34817162 -1.26423532 -0.92844848
## P11554_211 -1.20339737 -0.6762369 -0.03002233 -1.15349135 -1.02828287
## P11554_212 -0.37876146 -0.6762369 0.51282867 -1.45399091 -0.78349043
## P11554_213 0.13876202 1.3061125 -0.32932967 -0.24985020 0.01869556
## P11554_214 0.55702451 1.1429252 -1.20076351 -0.16074942 -0.28107285
## P11554_215 -0.04271474 -0.6762369 -0.29980703 0.18783666 -0.11191103
## P11554_216 -0.45803297 -0.6762369 -1.63710383 -1.04075925 -1.24544814
## P11554_217 0.15467100 1.1285955 -1.97301968 -0.97576982 -1.24050099
## P11554_218 0.15186512 -0.6762369 -1.23575799 -0.81592304 -1.05073886
## P11554_225 0.49672921 -0.6762369 0.53406628 1.11575394 0.94740403
## P11554_226 2.20693472 1.9933521 0.97590187 1.36090161 1.35147538
## P11554_227 2.17801544 1.1785206 1.90238590 1.53530417 1.43252628
## P11554_228 -1.10288806 -0.6762369 0.85398659 0.26854285 1.14688499
## P11554_229 -0.14989115 -0.6762369 0.67847930 1.19651714 1.25647988
## P11554_230 0.26514014 1.3653368 0.74603162 1.42547538 1.47438690
## AT5G61460 AT2G22010 AT4G37490 AT3G21870 AT1G47220 AT5G67380
## P11554_207 0.1690030 -0.06861385 -1.5354250 -0.593274 0.8495647 -0.7683708
## P11554_208 0.5745332 0.20512935 -0.2975766 -0.593274 0.9989809 -0.4959823
## P11554_209 0.4296886 -0.23228315 0.3193324 1.380750 -0.7614314 -0.7447125
## P11554_210 -1.1566688 -0.78179879 -0.1259733 -0.593274 -0.7614314 -1.0926322
## P11554_211 -1.3100682 -0.78677987 -0.5272018 1.581811 1.3632010 -0.5654162
## P11554_212 -0.9219234 -0.53977540 -0.3005791 -0.593274 -0.7614314 -0.5909952
## P11554_213 0.1434596 -0.50915673 -0.8766394 -0.593274 -0.7614314 -0.2852988
## P11554_214 0.3320849 0.27052089 0.6116538 1.823656 -0.7614314 -0.8509003
## P11554_215 0.2835217 -0.39345128 -0.2043430 -0.593274 -0.7614314 -0.5815864
## P11554_216 -1.6677165 -1.28954695 -0.3178121 -0.593274 -0.7614314 -0.8766509
## P11554_217 -1.4624459 -1.20022494 -1.3112611 -0.593274 -0.7614314 -0.7240461
## P11554_218 -1.2568870 -1.63614786 -1.5287794 -0.593274 0.8257927 -0.3937808
## P11554_225 0.9054863 1.28695770 1.5757732 -0.593274 1.3455171 1.1460560
## P11554_226 1.0073601 0.89586204 1.0773172 1.914987 1.6886488 1.5843314
## P11554_227 1.0946348 1.00235598 0.6717773 -0.593274 -0.7614314 1.7107005
## P11554_228 0.8349256 1.60905014 -0.2506158 1.011359 -0.7614314 0.8237013
## P11554_229 0.7664692 0.48918154 1.5685039 -0.593274 1.3040400 1.1710188
## P11554_230 1.2345427 1.67872117 1.4518489 -0.593274 -0.7614314 1.5345643
## AT2G26430 AT2G27960 AT5G22000 AT4G14220 AT2G23080
## P11554_207 -1.7459208 -1.02612106 -0.71969923 -0.25334034 -1.39657957
## P11554_208 -1.0512180 0.02624340 -0.43029242 -0.40018432 -1.04034844
## P11554_209 0.3004913 -0.40151646 0.76392231 0.44041176 -1.01623290
## P11554_210 -0.5247178 -0.05032417 -0.23571244 0.71708252 0.50490323
## P11554_211 -1.1026499 -0.14448016 -0.25415423 0.34757321 0.49091106
## P11554_212 -0.6386261 -0.17551821 -0.29940653 0.71782824 0.82795785
## P11554_213 -0.6220417 -1.24731273 -1.05936133 -2.66534199 -1.52576901
## P11554_214 -1.0581959 -1.40183359 -2.22351330 -1.55574679 -1.29709543
## P11554_215 -0.1027736 -1.72284836 -1.31615030 -1.32441492 -0.87694142
## P11554_216 -0.3862739 -0.15816120 -0.38724669 0.83193927 0.01608135
## P11554_217 0.4076203 -0.53995148 -0.05096494 -0.12556598 0.15936505
## P11554_218 -0.1280205 0.04255117 0.40821503 0.03690159 0.24331830
## P11554_225 0.5823014 0.88022870 0.14344025 0.40158951 0.06958938
## P11554_226 0.7879527 0.98822950 1.19251277 0.20947789 0.75903153
## P11554_227 1.7069688 1.86086711 1.41821162 1.23606136 0.89696507
## P11554_228 1.2894615 0.73717111 0.33959932 0.01711205 -0.02471837
## P11554_229 0.4871189 0.69475225 1.62251594 0.06227844 1.18526437
## P11554_230 1.7985235 1.63802417 1.08808415 1.30633847 2.02429794
## AT1G34460 AT5G48640 AT2G20580 AT1G14750 AT3G23580
## P11554_207 -0.93199178 -1.04072417 -1.11929270 -1.314156672 -0.28646242
## P11554_208 -0.60133724 -1.19910847 -0.91424775 -0.547558474 0.84570028
## P11554_209 -0.58308690 -0.98335185 -0.64039995 0.294893306 -0.40458334
## P11554_210 0.09492163 0.51298886 0.18659378 0.648454101 -0.19666603
## P11554_211 0.70207659 0.67750817 0.21981921 0.961171649 -0.53858578
## P11554_212 0.84080951 1.04905159 0.35133370 1.633524205 -0.09544559
## P11554_213 -1.52476760 -1.16073341 -1.32366814 0.009506058 -0.18193164
## P11554_214 -1.67517607 -1.86514394 -1.21978802 -1.188316776 -0.30886808
## P11554_215 -1.75632886 -1.32411200 -1.41770817 0.088360784 0.29669368
## P11554_216 0.36994794 0.64938323 -0.30305995 0.612056686 0.74369696
## P11554_217 0.70960521 0.56750363 -0.15942956 0.040589110 -0.39715550
## P11554_218 0.70117083 0.45430173 0.08206493 0.429170655 -0.14132834
## P11554_225 0.02066363 0.04359678 0.02962313 -2.512872642 -2.12617017
## P11554_226 0.66341246 -0.11675079 0.67639617 0.903809443 -1.01425145
## P11554_227 0.85900173 0.50381575 0.71730567 0.602581823 -0.84379847
## P11554_228 -0.49330902 0.71401652 1.28837928 -0.887194733 1.12235885
## P11554_229 1.12920648 1.58379968 1.75569682 0.654224632 1.05145614
## P11554_230 1.47518148 0.93395866 1.79038155 -0.428243157 2.47534091
## AT5G45190 AT1G73690 AT3G60550 AT5G07450 AT4G14150
## P11554_207 -1.483098611 0.5088373 0.5781832 -0.10498459 0.02290890
## P11554_208 0.148637149 1.1695896 1.3438869 0.02233586 0.69488222
## P11554_209 0.698661915 1.3752594 -0.8263181 0.10505007 -0.08306818
## P11554_210 0.432746813 1.2740239 -0.8263181 -0.70304603 -1.63241032
## P11554_211 0.253922787 0.4671904 -0.8263181 0.14003177 -0.04239288
## P11554_212 1.132546865 0.3774490 1.7096187 0.14000520 -0.49723616
## P11554_213 -0.001170315 0.2130767 0.7598300 0.21868667 1.06344358
## P11554_214 0.523908127 -0.2112003 0.6292581 -1.63877401 0.98024183
## P11554_215 -1.895935080 -0.9559733 -0.8263181 -0.13807204 1.62531557
## P11554_216 -1.198520307 -1.3449210 -0.8263181 -0.16142926 -0.64134538
## P11554_217 -0.922964825 -1.0784722 1.6743807 1.95933910 1.62283695
## P11554_218 -0.352680080 -0.7376110 0.5574582 0.78560589 0.69506375
## P11554_225 0.053227285 0.2438586 1.0105653 0.65619524 0.27660593
## P11554_226 -0.243605467 -2.1742626 -0.8263181 -2.75953113 -0.12102403
## P11554_227 -0.507106723 -0.7354943 -0.8263181 0.93509708 -1.11460894
## P11554_228 -0.075370450 0.8359823 -0.8263181 0.07835858 -0.02089426
## P11554_229 1.369671398 0.9576685 -0.8263181 0.52830339 -1.39422649
## P11554_230 2.067129520 -0.1850010 -0.8263181 -0.06317179 -1.43409208
## AT3G63120 AT4G34160 AT2G44740 AT4G03270 AT1G70210
## P11554_207 -0.2722386 0.005670564 0.07474432 0.75751400 1.28499699
## P11554_208 -0.3746982 -0.015473030 0.06630093 0.51696786 1.09522654
## P11554_209 -0.1218671 -0.035845268 0.20135161 0.70690708 0.50632874
## P11554_210 -0.8646246 -0.338371887 -0.85507389 1.05453600 0.99625142
## P11554_211 -0.5131288 -0.274964576 -0.92124385 -1.47602783 0.44631589
## P11554_212 -0.1099655 -0.418550803 -1.05724080 -1.47602783 0.66252391
## P11554_213 2.1711651 1.358685339 1.65551887 0.58367332 -0.73465239
## P11554_214 1.3871338 1.482018215 1.12502116 -1.47602783 -0.87007513
## P11554_215 1.5962102 1.507218219 1.35981463 0.46247955 -0.30133401
## P11554_216 1.0519375 1.057337702 1.45675094 1.25355215 1.36456590
## P11554_217 0.2942978 1.156017018 0.59172124 0.82047496 0.56979829
## P11554_218 0.8270841 0.934361430 0.78889426 0.72456962 0.28680618
## P11554_225 -0.6367489 -1.156178697 0.07117331 0.21086377 -0.06135774
## P11554_226 -0.4880779 -1.119046519 -0.75416174 0.48558615 -0.75105952
## P11554_227 -1.1649095 -0.841564978 -0.04773249 -1.47602783 -0.38360319
## P11554_228 -1.1458255 -1.293229391 -1.21333939 -0.22110582 -1.06151588
## P11554_229 -0.6894172 -0.950236586 -1.16803774 -1.47602783 -0.49624931
## P11554_230 -0.9463267 -1.057846751 -1.37446137 0.02412052 -2.55296673
## AT3G50070 AT2G45080 AT1G50240 AT1G76310 AT3G20150 AT2G17620
## P11554_207 0.20079650 0.2822414 -0.08751811 0.07300656 0.4504544 0.8748714
## P11554_208 0.49813288 0.1071033 0.64935806 0.57094205 0.6412934 0.7389339
## P11554_209 0.01380268 0.2144466 0.68484050 1.22577864 0.1301460 0.1068920
## P11554_210 0.71283662 0.5368599 0.11043846 0.11095866 1.2582951 0.9197302
## P11554_211 1.01333434 1.4025988 0.40245607 0.39996738 -0.1985455 0.6338477
## P11554_212 0.39083946 0.1014876 0.37674859 0.37109999 0.7291742 0.8807667
## P11554_213 0.40970262 0.1254039 0.76813298 0.83645301 0.1853557 0.1167484
## P11554_214 0.14109163 0.4940920 0.85666416 0.63365559 0.8706169 0.5086589
## P11554_215 -0.28456606 1.0990688 0.77533929 1.04356341 1.0733422 0.1802182
## P11554_216 1.51251815 1.5715490 1.08648986 0.43332152 0.6032732 1.0272144
## P11554_217 1.40662320 0.9670248 0.96786955 0.89755964 0.9489563 0.9258818
## P11554_218 1.14488180 0.0192316 0.94345103 0.99559348 0.6801133 0.8424683
## P11554_225 -1.25921105 -1.5760560 -1.96266255 -1.18083838 -2.0004966 -1.5421722
## P11554_226 -1.14896918 -1.7793381 -1.63877405 -1.66022309 -1.5443865 -1.0348306
## P11554_227 -1.70277969 -1.6185990 -1.04281336 -0.77253400 -1.4474843 -0.8330483
## P11554_228 -1.34557863 -0.3710423 -1.29195009 -1.76593218 -1.1324175 -1.0119247
## P11554_229 -0.61597610 -0.5950755 -0.42350696 -0.67721335 -0.6257899 -1.6453350
## P11554_230 -1.08747916 -0.9809969 -1.17456343 -1.53515894 -0.6219003 -1.6889211
## AT5G06150 AT4G35620 AT1G53140 AT1G05440 AT3G23890 AT1G44110
## P11554_207 0.9820362 1.0759684 0.39175714 0.6913499 0.4747263 0.93283443
## P11554_208 0.8137129 0.8378269 0.78179429 1.0107677 1.2923942 1.35918495
## P11554_209 0.5828501 0.3696383 0.43484096 1.4406834 0.9777198 1.05602781
## P11554_210 0.5191027 0.4769892 0.22532923 0.9525019 0.4539379 0.62617353
## P11554_211 0.4330203 0.5977430 -0.00813146 0.5252172 0.1975577 0.42756483
## P11554_212 0.3746919 0.8777562 0.95345150 -0.1010815 0.4311020 0.32853271
## P11554_213 0.7399072 0.3738371 1.11920677 1.3052538 0.6447525 0.47831372
## P11554_214 0.5523373 0.9277422 1.06008994 0.2793860 1.1789711 1.07093151
## P11554_215 0.3173754 -0.0385376 0.45497863 0.2978220 0.6397487 0.46625017
## P11554_216 0.8922405 0.9699053 1.00133897 0.2821980 0.6002678 0.70911173
## P11554_217 0.9287031 0.7714122 1.01435747 0.5395334 0.6567489 0.15044727
## P11554_218 0.9168378 0.4789071 0.21395967 0.2336478 0.3635734 0.09817155
## P11554_225 -1.4508674 -0.8174181 -1.36682438 -0.9852936 -1.4533920 -1.02018349
## P11554_226 -1.3768268 -1.3844367 -1.14082651 -1.4383497 -1.4584113 -1.56596547
## P11554_227 -1.1983138 -1.1313941 -0.99607502 -1.0729914 -1.0705713 -0.97802545
## P11554_228 -1.4763080 -1.5939270 -1.59591057 -0.9503456 -1.2887196 -1.55503602
## P11554_229 -1.0351244 -0.8583330 -0.78051764 -1.8992611 -1.4728318 -1.01909161
## P11554_230 -1.5153750 -1.9336793 -1.76281900 -1.1110385 -1.1675742 -1.56524216
## AT3G11520 AT4G26660 AT1G03780 AT3G51280 AT2G26760 AT1G20610
## P11554_207 0.9046195 0.5097368 0.53760813 0.8898906 0.98997545 1.21855586
## P11554_208 1.1769606 1.0777019 0.75933169 0.8113518 1.37354037 1.54107242
## P11554_209 0.6403287 0.6283999 0.81923249 0.9767962 0.92667582 1.19361182
## P11554_210 0.3683880 0.1225244 0.03242994 0.2308941 0.13681106 0.23635286
## P11554_211 0.4774566 0.2638093 0.39711162 0.2257577 0.70537668 0.14332966
## P11554_212 0.6251957 0.5613660 0.75816240 0.4075570 0.41386539 0.84293901
## P11554_213 0.3955908 0.7229974 0.85744856 0.7921499 0.36547599 0.48210535
## P11554_214 1.0186098 1.0105923 0.66439273 1.0060805 1.17768185 0.91791948
## P11554_215 0.7339342 0.6757324 0.98226037 0.8636822 0.54578135 0.55853687
## P11554_216 0.3139828 0.9693917 0.93583105 0.7799263 -0.02996059 0.03830312
## P11554_217 0.7579921 0.5125464 0.71227313 0.2210682 0.36841516 0.36458906
## P11554_218 0.4839872 0.8885172 0.56033352 0.7783524 0.58988620 -0.37310024
## P11554_225 -0.7515595 -1.3182256 -1.25754505 -1.4143286 -1.16890803 -1.58935161
## P11554_226 -1.5839100 -1.0794040 -1.39697666 -1.1902208 -0.66701574 -0.92201457
## P11554_227 -1.4797216 -1.1266223 -1.01536198 -1.3437654 -1.01957122 -0.71164625
## P11554_228 -1.3994955 -1.5512432 -1.40545682 -1.2450464 -1.73404002 -1.28876939
## P11554_229 -1.0475286 -1.2092823 -1.35447664 -1.3195668 -1.44178399 -1.00467607
## P11554_230 -1.6348309 -1.6585383 -1.58659848 -1.4705789 -1.53220571 -1.64775738
## AT1G59540 AT4G21820 AT5G63950 AT5G10440 AT1G80370
## P11554_207 0.89838602 0.3961242 0.24195515 0.36264158 0.59868208
## P11554_208 0.90761152 0.8168150 1.75196736 0.51785005 0.60517738
## P11554_209 0.85293264 0.9295113 1.20202743 1.90369639 2.08708660
## P11554_210 -0.21382820 0.0488946 -0.08229845 -0.47880735 0.76087921
## P11554_211 -0.18095297 0.3247095 0.41721309 -2.10707586 -0.57376766
## P11554_212 0.13412257 0.1906130 0.08753884 0.31694616 0.50654728
## P11554_213 1.09666630 1.5870220 0.42581077 -0.84710464 0.30893992
## P11554_214 1.77799150 1.2574531 0.45992408 0.29152589 0.57361981
## P11554_215 0.92163613 0.9007700 1.05492810 2.16196719 0.77315241
## P11554_216 0.63155658 0.1953830 -0.12780162 0.61018777 -1.26109231
## P11554_217 0.33528696 0.6154065 0.34619345 -0.22876546 -0.04326273
## P11554_218 -0.06332676 0.2466365 0.26118091 -0.14000334 0.45252299
## P11554_225 -1.31176673 -1.6206249 -2.29152000 0.04471264 -1.41768096
## P11554_226 -0.83269463 -0.9055910 -1.81331732 -0.65112221 -0.22501959
## P11554_227 -1.43072396 -1.0444621 -1.10107850 0.13036454 -0.40643614
## P11554_228 -1.52820159 -1.1091011 -0.36245902 -0.68033377 -0.77836397
## P11554_229 -0.87351120 -1.4783175 -0.75237006 -0.03237705 0.28069748
## P11554_230 -1.12118416 -1.3512421 0.28210578 -1.17430253 -2.24168178
## AT5G09790 AT1G68310 AT5G67260 AT5G48630 AT2G31320
## P11554_207 0.62625910 0.84139146 0.16770684 2.009509945 0.6746070
## P11554_208 -0.14761359 0.86967773 0.62003491 0.816960411 0.7602131
## P11554_209 1.49238745 1.55849836 0.79427538 0.691072928 1.4915479
## P11554_210 -0.54491353 -0.32151871 -0.19736573 -1.093407231 -1.7181133
## P11554_211 -0.34871482 -0.59454483 0.54270955 -0.480111824 -0.5416318
## P11554_212 -0.52313099 -0.88258337 -0.91962906 -0.510341823 -0.2930092
## P11554_213 1.31065067 0.52459402 0.48356712 0.629086207 2.0062609
## P11554_214 -0.01741395 1.41074721 1.59334443 1.140854879 0.9813375
## P11554_215 2.06267110 1.80995000 2.41155440 1.640009515 1.1176996
## P11554_216 -1.09266850 -0.82920263 -1.26881538 -0.727769109 -1.6263809
## P11554_217 -0.95564998 -1.41411033 -0.97239779 -1.282451561 -0.4775084
## P11554_218 -0.36067895 -0.96117382 -1.12879120 -0.860954698 -0.9091896
## P11554_225 -0.28194034 -0.51624560 -0.45693272 -0.622501960 -0.2039350
## P11554_226 -1.16120660 -0.01750975 0.53611587 0.439846310 -0.1909670
## P11554_227 -0.69146531 -0.23124104 -0.50190041 0.163506510 0.0143302
## P11554_228 1.15319615 -1.52776915 -1.17356446 -1.364339397 -0.3172102
## P11554_229 0.76130000 0.25157872 -0.04840687 -0.598863126 -0.3936088
## P11554_230 -1.28106793 0.02946170 -0.48150486 0.009894024 -0.3744421
## AT5G57590 AT4G19560 AT5G40840 AT2G31270 AT3G23740 AT1G69770
## P11554_207 0.33077296 0.4562264 0.4397473 1.3302474 1.3396367 1.2168231
## P11554_208 1.01305315 1.2952824 1.0317361 1.1977920 1.1426616 1.1287121
## P11554_209 1.38282436 1.5855190 0.7239700 1.0730228 1.1358363 1.1008244
## P11554_210 -1.10749373 -1.1465668 -0.5151019 -0.3970551 -0.4354116 -0.4566175
## P11554_211 -0.13079827 -0.2751132 -1.0933676 -0.4924679 -0.4941302 -0.5338723
## P11554_212 -0.15301050 -1.0253843 0.4028398 -0.3826736 -0.5087725 -0.5311471
## P11554_213 0.83317607 0.6887389 1.1733657 1.4371205 1.4679987 1.5417596
## P11554_214 1.41155987 1.7808829 1.5363580 1.4683452 1.5345695 1.5372370
## P11554_215 1.89383227 0.3766625 2.1039031 1.5002337 1.4725056 1.5402341
## P11554_216 -1.86180614 -0.6860718 -0.4173033 -0.4672640 -0.5500514 -0.4820198
## P11554_217 -0.62143861 -1.2303247 0.1812927 -0.6042890 -0.6059442 -0.5217882
## P11554_218 -1.01978238 -0.2212008 -0.9112168 -0.5407428 -0.5229375 -0.5244628
## P11554_225 0.03681596 0.3554095 -0.4021719 -0.5467487 -0.5575552 -0.6429901
## P11554_226 -0.63700616 -1.4167558 -0.6784010 -0.6233182 -0.7679564 -0.6681518
## P11554_227 0.30780827 1.0403819 -0.8566529 -0.6736884 -0.7013962 -0.6942066
## P11554_228 -0.71739796 -0.1036497 -0.5725964 -1.0264521 -0.9312076 -0.9726310
## P11554_229 -0.62354879 -0.6266338 -1.5242118 -1.2234305 -1.0113743 -1.0494889
## P11554_230 -0.33756039 -0.8474026 -0.6221891 -1.0286311 -1.0064714 -0.9882142
## AT1G78650 AT1G75150 AT2G24490 AT5G08020 AT2G29680 AT1G07370
## P11554_207 1.4141495 1.3328203 1.3906610 1.3098072 1.3123103 1.2479632
## P11554_208 1.0282194 1.3263445 1.2687255 1.2122490 1.2607842 1.2638634
## P11554_209 1.1333030 1.1951879 1.2807546 1.2485153 1.3347890 1.2012186
## P11554_210 -0.5104543 -0.6074271 -0.5998294 -0.6317226 -0.6985314 -0.7477878
## P11554_211 -0.6447993 -0.6300011 -0.5995103 -0.5633658 -0.6079118 -0.6799448
## P11554_212 -0.3538967 -0.4453156 -0.5244005 -0.5783329 -0.5990920 -0.5499127
## P11554_213 1.4892314 1.3633436 1.3542183 1.3925527 1.3951124 1.5383430
## P11554_214 1.4055897 1.5602290 1.3539319 1.4851550 1.4117129 1.4048909
## P11554_215 1.6149815 1.3980083 1.4659468 1.4855806 1.4315581 1.4694567
## P11554_216 -0.8162330 -0.6435570 -0.6457795 -0.5645983 -0.5608253 -0.5358026
## P11554_217 -0.6020175 -0.6711028 -0.4058549 -0.6002815 -0.5752535 -0.5539846
## P11554_218 -0.6038185 -0.7054308 -0.4858176 -0.5847791 -0.5395682 -0.5138255
## P11554_225 -0.8077796 -0.5713384 -0.6618007 -0.4472875 -0.5844514 -0.6093448
## P11554_226 -0.5920079 -0.6205128 -0.5631934 -0.5694748 -0.5384633 -0.5576318
## P11554_227 -0.4520264 -0.6869229 -0.6241822 -0.6568106 -0.5200568 -0.5070446
## P11554_228 -0.9560058 -0.8372961 -0.9212376 -0.9987128 -0.9268903 -1.0253172
## P11554_229 -0.9621202 -0.7478257 -0.9274583 -0.9780567 -0.9157106 -0.8042870
## P11554_230 -0.7843153 -1.0092033 -1.1551737 -0.9604372 -1.0795122 -1.0408525
## AT5G43080 AT1G02970 AT5G02520 AT4G37630 AT1G07270 AT1G67320
## P11554_207 1.5053354 1.1895016 1.3095250 1.2815772 1.1565064 1.3475981
## P11554_208 1.3531769 1.0402703 1.3714185 1.3514580 1.4898554 1.3123250
## P11554_209 1.1015110 1.1932780 1.3639613 1.1464008 1.2629070 1.4930854
## P11554_210 -0.6081216 -0.6194429 -0.5063147 -0.4592652 -0.3041721 -0.5616834
## P11554_211 -0.6275332 -0.5887447 -0.3262023 -0.4805167 -0.7005725 -0.4360939
## P11554_212 -0.5034924 -0.3951856 -0.1291863 -0.4058663 -0.4667231 -0.3557620
## P11554_213 1.2535882 1.6631276 1.1536365 1.1943414 1.5208519 1.3815020
## P11554_214 1.2715294 1.1924788 1.1323069 1.7085906 1.3455930 1.2487143
## P11554_215 1.6005143 1.6693528 1.5778187 1.2693137 1.2250741 1.2998709
## P11554_216 -0.4821917 -0.5408598 -0.5578037 -0.4994367 -0.3937957 -0.6215555
## P11554_217 -0.5366754 -0.6340409 -0.3368507 -0.8038876 -0.4408790 -0.5636698
## P11554_218 -0.4806124 -0.8083424 -0.8315809 -0.5562516 -0.6006485 -0.4518079
## P11554_225 -0.5795354 -0.1846441 -0.8509071 -0.4219436 -0.5598631 -0.6946568
## P11554_226 -0.6251193 -0.5747512 -0.6355880 -0.5249162 -0.4686905 -0.5929288
## P11554_227 -0.7294767 -0.5237745 -0.5099174 -0.4598810 -0.8448752 -0.7258497
## P11554_228 -1.0117148 -1.0744005 -0.9570335 -0.9514355 -1.0707538 -1.1195479
## P11554_229 -0.7488276 -1.1877300 -1.3228988 -1.3084272 -1.1373349 -0.9674317
## P11554_230 -1.1523545 -0.8160923 -0.9443836 -1.0798539 -1.0124794 -0.9921084
## AT5G48600 AT3G24495 AT1G44900 AT5G63920 AT1G65470 AT3G02820
## P11554_207 1.1850839 1.1759085 1.2871712 1.1110978 1.2274634 1.3577399
## P11554_208 1.4112412 1.3129506 1.3404583 1.3349649 1.3571820 1.2717266
## P11554_209 1.2979243 1.3620853 1.3362781 1.4055262 1.2213711 1.3521512
## P11554_210 -0.4601231 -0.5086609 -0.5291033 -0.5359858 -0.6839690 -0.5841437
## P11554_211 -0.5431664 -0.5744437 -0.4760306 -0.5269688 -0.4848924 -0.4482701
## P11554_212 -0.3626244 -0.3793020 -0.3959850 -0.3857805 -0.3272211 -0.4300846
## P11554_213 1.3788438 1.4568398 1.3619726 1.3414047 1.3716821 1.2426448
## P11554_214 1.3865620 1.3683543 1.3705471 1.5132862 1.3518045 1.2829005
## P11554_215 1.4561109 1.4233484 1.3836663 1.3596463 1.5727082 1.6006804
## P11554_216 -0.6694035 -0.4544018 -0.5496704 -0.5300699 -0.5335871 -0.5122108
## P11554_217 -0.5402411 -0.6087522 -0.5200249 -0.5065896 -0.5595543 -0.5807392
## P11554_218 -0.5947747 -0.5533049 -0.4627397 -0.4046068 -0.6284792 -0.5199123
## P11554_225 -0.8902324 -0.7099810 -0.6518325 -0.7656418 -0.6492096 -0.7635414
## P11554_226 -0.6540643 -0.6408921 -0.6598547 -0.6934622 -0.6164777 -0.6878525
## P11554_227 -0.5556733 -0.6273739 -0.6669496 -0.6733024 -0.6416414 -0.6298736
## P11554_228 -1.0114518 -0.9496034 -1.0508446 -1.1549999 -0.9253341 -0.9879674
## P11554_229 -0.9858013 -1.0748779 -1.1373090 -1.0363476 -1.0217611 -1.0343790
## P11554_230 -0.8482098 -1.0178932 -0.9797493 -0.8521707 -1.0300845 -0.9288688
## AT3G18524 AT2G07690 AT2G16440 AT5G46280 AT1G67630 AT2G40550
## P11554_207 1.0813158 1.2655021 1.3113914 1.2840035 1.2757878 1.2249216
## P11554_208 1.1793649 1.3002909 1.3040662 1.4012114 1.4147095 1.3475759
## P11554_209 1.4516359 1.3194267 1.3335481 1.3744306 1.4695292 1.3859945
## P11554_210 -0.8033740 -0.5730487 -0.5938695 -0.6071882 -0.5756564 -0.5440521
## P11554_211 -0.5294062 -0.4611332 -0.5494372 -0.5419400 -0.5893138 -0.4626213
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## P11554_213 1.4989032 1.3919045 1.3351264 1.2893939 1.3049248 1.4201793
## P11554_214 1.4934262 1.3761327 1.3690947 1.3415019 1.3345465 1.3664964
## P11554_215 1.3899007 1.4379469 1.4326163 1.4349610 1.3331947 1.3784274
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## P11554_230 -0.9243323 -0.9576831 -0.9841195 -0.9601884 -0.9647698 -0.9482602
## AT5G67100 AT1G04020 AT1G47210 AT3G42660 AT2G36010 AT1G78770
## P11554_207 1.2755957 1.2353125 1.4047305 1.2026529 1.0097221 1.0911893
## P11554_208 1.3579576 1.5066604 1.2574210 1.3543728 1.3123304 1.3025314
## P11554_209 1.3466087 1.3197322 1.2000855 1.3296797 1.3589766 1.3054000
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## P11554_213 1.3860082 1.3941574 1.3188821 1.3344438 1.4484702 1.1728965
## P11554_214 1.3966324 1.2652945 1.4312309 1.3634470 1.4076514 1.4445825
## P11554_215 1.3700702 1.3481022 1.3743743 1.4178038 1.4692128 1.6174674
## P11554_216 -0.6628502 -0.6211426 -0.5567971 -0.6261368 -0.5164869 -0.7129891
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## AT5G27680 AT5G62410 AT1G01370 AT4G02460 AT4G29170 AT1G18040
## P11554_207 1.1834485 0.9984663 1.0774924 1.1040710 1.1230335 0.9651769
## P11554_208 1.2818980 1.1344067 0.9760469 1.1458063 1.0781275 0.4599297
## P11554_209 0.9135632 1.2260337 1.3844050 1.5061699 1.3429584 1.2333857
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## P11554_213 1.3920407 1.1374980 1.6468283 1.3806348 1.3685896 1.6969431
## P11554_214 1.8553264 1.6968836 1.1982197 1.3223978 1.1870458 1.3690402
## P11554_215 1.3698353 1.6769697 1.6721586 1.4811517 1.8202573 1.8642781
## P11554_216 -0.6733442 -0.7732624 -0.5492081 -0.6866920 -0.5405523 -0.7070610
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## P11554_226 -0.6522701 -0.6897992 -0.9305390 -0.9143301 -0.7883706 -0.7747897
## P11554_227 -0.6952287 -0.6167416 -0.5722250 -0.5973125 -0.6527395 -0.6655631
## P11554_228 -1.0737888 -1.0435267 -1.1861148 -1.2898066 -0.8788921 -1.3750011
## P11554_229 -0.9479239 -1.1572843 -0.6316731 -0.7971661 -1.2688503 -0.9367031
## P11554_230 -0.7193694 -0.9669614 -0.9242798 -0.8471189 -0.8901463 -0.4277392
## AT2G22490 AT1G22270 AT2G45280 AT5G20850 AT5G49010 AT4G02070
## P11554_207 1.3144516 1.06824591 1.30985874 1.2344818 1.3188876 1.1926144
## P11554_208 1.2748486 1.58755775 1.49233275 1.3573137 1.5060545 1.4781713
## P11554_209 1.3269560 0.95597758 1.47949415 1.3126489 1.1701549 1.4298551
## P11554_210 -0.7694982 -0.98288870 -0.59761362 -0.6501801 -0.5408709 -0.7665759
## P11554_211 -0.9951765 -0.95089199 -0.84300695 -0.8350804 -0.5636194 -0.3843178
## P11554_212 -0.8502410 -0.72936634 -0.67858027 -0.8636645 -0.4222908 -0.5456866
## P11554_213 1.1407099 1.65510672 1.20630862 1.3191133 1.3280741 1.2985871
## P11554_214 1.0778910 1.31220758 1.25375319 1.5837739 1.1839520 1.3495335
## P11554_215 1.3467505 1.24789252 1.22791326 1.2564353 1.4467240 1.2721459
## P11554_216 -0.8905908 -0.63674531 -0.98461362 -0.7496484 -0.6514836 -0.7263330
## P11554_217 -1.0292782 -0.61475576 -0.87258857 -0.6992725 -0.9014903 -0.8289585
## P11554_218 -0.9225590 -0.86461862 -0.68009370 -0.9737973 -0.6166682 -0.6638184
## P11554_225 0.1286944 -0.32366601 -0.26523366 -0.3502298 -0.6951958 -0.3241191
## P11554_226 0.2185094 -0.03141229 -0.07700316 -0.2635790 -0.2053196 -0.4107060
## P11554_227 0.3045108 -0.31406875 -0.25928487 -0.3659977 -0.1685324 -0.3772035
## P11554_228 -1.0825456 -0.80103748 -0.79753763 -0.6711928 -1.1545816 -0.9678112
## P11554_229 -0.7666137 -0.35140028 -0.94452627 -1.0387349 -1.0589173 -1.2676605
## P11554_230 -0.8268191 -1.22613653 -0.96957839 -0.6023894 -0.9748771 -0.7577167
## AT3G24320 AT4G18470 AT3G27060 AT3G12280 AT5G25380 AT5G11300
## P11554_207 1.1626967 1.2848857 1.3315667 1.2180682 1.44875190 1.049002387
## P11554_208 1.1384927 1.3626590 1.4427012 1.3145524 1.51760819 1.197944880
## P11554_209 1.2889553 1.4616110 1.3968832 1.4049859 1.33295605 1.659417336
## P11554_210 -0.6203197 -0.4160826 -0.6069181 -0.4692371 -1.21369542 -0.411449502
## P11554_211 -0.5563531 -0.6076801 -0.5930519 -0.3220217 0.41226075 -0.214740878
## P11554_212 -0.5280890 -0.4224114 -0.5880054 -0.3519301 0.24325734 0.005289071
## P11554_213 1.4706251 1.3902503 1.3678835 1.3580634 0.91752489 0.726644737
## P11554_214 1.5187300 1.3156359 1.3365121 1.3919969 1.00433331 0.971705203
## P11554_215 1.3622487 1.2654145 1.2770265 1.3784434 -0.24668989 -0.467171190
## P11554_216 -0.8119189 -0.8030250 -0.8297179 -0.9213681 -0.43313901 -0.051925246
## P11554_217 -1.0623907 -0.5667648 -0.8827988 -0.9095040 -0.28212550 -0.126494571
## P11554_218 -0.6925845 -0.9083230 -0.8700503 -0.8889345 -0.82193795 -0.406208957
## P11554_225 -0.2085169 -0.3749001 -0.3969610 -0.6024969 0.01869071 0.434876032
## P11554_226 -0.3614163 -0.5303188 -0.4347964 -0.4490950 -0.51314465 -0.168788659
## P11554_227 -0.1504663 -0.5003786 -0.4741663 -0.4573603 -0.12271563 0.781527549
## P11554_228 -0.9647043 -0.9342504 -0.8101530 -0.9310099 -0.45024097 -2.093883964
## P11554_229 -1.1093620 -1.0330027 -0.8362733 -0.9890961 -2.36255696 -1.093053219
## P11554_230 -0.8756267 -0.9833190 -0.8296808 -0.7740564 -0.44913719 -1.792691008
## AT2G33560 AT4G04950 AT1G57820 AT1G77390 AT1G16330 AT4G09140
## P11554_207 1.41126316 1.0501997 0.3595012 0.8386156 0.9863955 1.16432028
## P11554_208 1.50262609 1.7546343 0.9980755 1.0513046 0.9223249 0.61578952
## P11554_209 1.81226306 1.6901801 1.3659949 0.4720732 0.2981498 0.53412202
## P11554_210 -0.42725931 -1.0713118 -0.7097144 -0.2740401 -0.7236422 -0.51952220
## P11554_211 0.09459429 -0.1814777 -0.7075302 -0.3083121 -0.7764358 -0.34298695
## P11554_212 -0.08948436 -0.8767922 -0.4287885 -0.8286207 0.1192896 -0.01888032
## P11554_213 0.37661873 0.7460613 1.3732173 1.4200670 1.6408418 2.24052600
## P11554_214 1.62539221 0.9448484 1.5306195 1.2569091 1.4490535 0.20238236
## P11554_215 0.14287436 0.9753433 1.2481212 2.0862405 1.4379631 1.75040033
## P11554_216 -0.84053714 -1.2743167 -0.2094874 -0.1488586 0.3021918 -0.32366186
## P11554_217 -0.23596231 -0.3604643 0.2428382 0.3711603 0.2563161 -0.71529881
## P11554_218 -0.24844953 -0.2962092 0.4524641 -0.1369152 0.3550813 0.50092426
## P11554_225 -0.42952754 0.2753321 -1.7248064 -1.0846331 -0.9882828 -1.34854710
## P11554_226 -0.37928451 -0.1784720 -0.9743803 -0.7793951 -1.3452959 -1.25569272
## P11554_227 -0.80138412 -0.2739323 -1.3859117 -0.8982927 -1.3032496 -0.74095895
## P11554_228 -1.77048589 -1.6438301 -0.8391944 -1.2010182 -0.9006643 -1.20093724
## P11554_229 -0.78818758 -0.4579440 -0.2596083 -1.2822556 -0.7906631 -0.08886322
## P11554_230 -0.95506960 -0.8218490 -0.3314103 -0.5540290 -0.9393737 -0.45311541
## AT2G40030 AT1G15570 AT2G27040 AT5G27620 AT1G09450
## P11554_207 0.56608029 0.46064213 0.41763475 0.9342171 1.14067060
## P11554_208 0.05880319 0.43332867 0.80432846 0.9146160 1.01761081
## P11554_209 1.51715672 0.84901891 0.97810208 0.8259398 0.45465578
## P11554_210 -0.27870976 -0.59369843 -0.80293132 -0.3851983 -0.89141769
## P11554_211 -0.22305292 -0.24856361 -0.64779678 -0.3171089 -0.09576789
## P11554_212 -0.18699911 0.23607132 -0.42616786 -0.3382805 -0.22788708
## P11554_213 1.89461381 1.93357696 1.79610316 1.9128809 1.65709160
## P11554_214 1.29780657 0.98546148 1.49547662 1.5621178 1.79001639
## P11554_215 1.44326073 1.66799152 1.67298644 1.5064889 1.55472045
## P11554_216 -0.36682827 -0.18805666 -0.33735093 -0.6337651 -0.31097454
## P11554_217 0.15263407 0.04374320 0.24673487 -0.4041156 -0.65062580
## P11554_218 0.36237603 0.01812318 -0.07633598 -0.7555659 -0.34015336
## P11554_225 -0.90909401 -0.27234408 -0.57290586 -0.4006308 -0.63725106
## P11554_226 -0.97545577 0.02800932 -0.37937398 -0.7261356 -1.21314308
## P11554_227 -0.89783312 -0.71080782 -0.36750535 -0.2745270 -0.76254832
## P11554_228 -1.12269707 -1.58582312 -1.17399648 -1.0018850 -0.91513172
## P11554_229 -1.13351249 -1.29075487 -1.09200549 -1.0551291 -0.59930136
## P11554_230 -1.19854889 -1.76591812 -1.53499634 -1.3639189 -0.97056373
## AT3G03130 AT1G10780 AT5G24330 AT1G47230 AT5G65420 AT5G55820
## P11554_207 1.3152889 0.96366371 1.2888296 1.3625787 1.3614326 0.83872398
## P11554_208 1.1753497 1.21572310 1.2043172 0.9566839 1.2182583 1.40167700
## P11554_209 1.0348202 1.01234774 1.0544269 0.7367921 0.7799337 0.82040360
## P11554_210 -0.5309712 -0.42377848 -0.1860195 -0.4134364 -0.6033322 -0.76294370
## P11554_211 -0.1364929 -0.32679299 -0.4073640 -0.2504996 -0.1943297 -0.26969501
## P11554_212 -0.0760110 -0.49900215 -0.3820900 -0.3048093 -0.2082269 -0.12026279
## P11554_213 1.5018049 1.81006236 1.4167994 1.5868203 1.3673075 1.41175653
## P11554_214 1.2950956 1.46552387 1.3931708 1.4734989 1.5599598 1.52272518
## P11554_215 1.2593250 1.26056609 1.5193153 1.5342216 1.2934116 1.40333433
## P11554_216 -0.1838422 -0.06356344 -0.2419728 -0.1962202 -0.2440769 0.08874210
## P11554_217 -0.1840496 -0.26787376 -0.3198303 -0.1813561 -0.3829422 0.04399071
## P11554_218 -0.2915297 -0.26121240 -0.5759900 -0.2869313 -0.1192221 -0.35275466
## P11554_225 -0.9389125 -0.77479754 -0.9324264 -0.9367352 -0.6039694 -0.56405649
## P11554_226 -0.8150359 -1.10248123 -0.7521130 -0.8295312 -0.6574796 -0.93819943
## P11554_227 -0.9178298 -0.92061846 -0.7676448 -0.9116850 -0.6032426 -0.85492408
## P11554_228 -1.4044524 -1.17752755 -1.1129111 -0.9353934 -1.3835633 -1.29380328
## P11554_229 -0.6845268 -0.92680555 -1.0730499 -1.2193252 -1.3584111 -1.46242494
## P11554_230 -1.4180303 -0.98343332 -1.1254472 -1.1846727 -1.2215076 -0.91228906
## AT3G49250 AT3G06030 AT5G43990 AT5G13960 AT2G38620 AT2G21800
## P11554_207 0.76182230 0.82102481 0.7567798 1.0043766 0.7091498 0.98031067
## P11554_208 1.00506220 1.01684596 0.6818722 1.3085413 1.2314364 0.86645912
## P11554_209 0.76986399 1.00721144 1.4158619 1.4788660 1.4824083 0.89846035
## P11554_210 -0.61754522 0.13697024 -0.7708602 -0.5948637 -0.4866701 0.11707096
## P11554_211 0.26859315 -0.20095345 -0.2919399 -0.3661511 -0.2831517 0.12366472
## P11554_212 -0.37966898 -0.16430412 -0.1086582 -0.2414945 -0.3545030 -0.10634112
## P11554_213 1.28148975 1.31455475 1.5458765 1.4390728 1.0683594 0.85496018
## P11554_214 1.75177795 1.41512011 1.7256013 1.2730129 1.5766051 1.64123137
## P11554_215 1.31526822 1.31921314 1.3918337 1.2866363 1.3268581 1.69749942
## P11554_216 0.08304583 -0.05486705 -0.3844021 -0.4534059 -0.1902658 -0.61084252
## P11554_217 0.16784242 -0.41115768 -0.1878223 -0.4221551 -0.2607280 -0.55744749
## P11554_218 -0.10292561 0.49781283 -0.3128184 -0.1337019 0.2311204 -0.23205276
## P11554_225 -1.34319574 -0.90703677 -1.2424826 -0.8574390 -0.9976361 -1.76136457
## P11554_226 -0.62472957 -0.82439278 -0.5601860 -0.7709018 -0.5765403 -1.16020415
## P11554_227 -0.37228891 -0.78627833 -0.3562295 -0.3838525 -0.5334090 -0.02943785
## P11554_228 -1.10646208 -1.48840682 -1.2494431 -1.3729869 -1.3054479 -0.73181780
## P11554_229 -1.21526705 -0.93162464 -1.1446612 -0.9757506 -1.3047874 -0.53051700
## P11554_230 -1.64268264 -1.75973165 -0.9083218 -1.2178030 -1.3327982 -1.45963154
## AT2G01905 AT2G07170 AT2G36200 AT2G32590
## P11554_207 1.710046799 1.16246877 0.789928494 0.9158040
## P11554_208 1.506037689 1.21521868 1.147157823 1.1134653
## P11554_209 1.267988288 1.21044060 1.240633443 1.2933929
## P11554_210 -0.329109796 -0.66107760 -0.023104453 -0.7870728
## P11554_211 -0.317900163 -0.12282299 -0.068006674 -0.1643060
## P11554_212 -0.005811059 0.10803380 -0.008155888 -0.2244563
## P11554_213 1.323202721 0.86065807 1.286910857 1.4311164
## P11554_214 0.827546245 1.47539009 1.451908875 1.1000030
## P11554_215 0.974138470 1.28567065 1.477508447 1.7474341
## P11554_216 -0.254739310 -0.12647254 -0.450342300 -0.3377033
## P11554_217 -0.976653536 0.05602871 -0.267145883 -0.5916351
## P11554_218 -0.323381468 0.23599004 -0.051833089 -0.1548873
## P11554_225 -1.281943965 -1.08364674 -1.305396182 -1.3558185
## P11554_226 -1.335965008 -1.05232203 -1.301268083 -0.9238693
## P11554_227 -0.609962188 -1.13010657 -1.127871684 -0.6470324
## P11554_228 -0.903000271 -1.31162882 -1.059346613 -1.4871688
## P11554_229 -0.462472609 -1.24453093 -0.846733569 -0.4577732
## P11554_230 -0.808020837 -0.87729120 -0.884843523 -0.4694927
##
## $`GO:0051726`$rowDendrogram
## 'dendrogram' with 2 branches and 140 members total, at height 3.94569
##
## $`GO:0051726`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0051726`$breaks
## [1] -2.75953113 -2.70434051 -2.64914989 -2.59395927 -2.53876864 -2.48357802
## [7] -2.42838740 -2.37319678 -2.31800615 -2.26281553 -2.20762491 -2.15243429
## [13] -2.09724366 -2.04205304 -1.98686242 -1.93167179 -1.87648117 -1.82129055
## [19] -1.76609993 -1.71090930 -1.65571868 -1.60052806 -1.54533744 -1.49014681
## [25] -1.43495619 -1.37976557 -1.32457494 -1.26938432 -1.21419370 -1.15900308
## [31] -1.10381245 -1.04862183 -0.99343121 -0.93824059 -0.88304996 -0.82785934
## [37] -0.77266872 -0.71747810 -0.66228747 -0.60709685 -0.55190623 -0.49671560
## [43] -0.44152498 -0.38633436 -0.33114374 -0.27595311 -0.22076249 -0.16557187
## [49] -0.11038125 -0.05519062 0.00000000 0.05519062 0.11038125 0.16557187
## [55] 0.22076249 0.27595311 0.33114374 0.38633436 0.44152498 0.49671560
## [61] 0.55190623 0.60709685 0.66228747 0.71747810 0.77266872 0.82785934
## [67] 0.88304996 0.93824059 0.99343121 1.04862183 1.10381245 1.15900308
## [73] 1.21419370 1.26938432 1.32457494 1.37976557 1.43495619 1.49014681
## [79] 1.54533744 1.60052806 1.65571868 1.71090930 1.76609993 1.82129055
## [85] 1.87648117 1.93167179 1.98686242 2.04205304 2.09724366 2.15243429
## [91] 2.20762491 2.26281553 2.31800615 2.37319678 2.42838740 2.48357802
## [97] 2.53876864 2.59395927 2.64914989 2.70434051 2.75953113
##
## $`GO:0051726`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0051726`$colorTable
## low high color
## 1 -2.75953113 -2.70434051 #0000FF
## 2 -2.70434051 -2.64914989 #0505FF
## 3 -2.64914989 -2.59395927 #0A0AFF
## 4 -2.59395927 -2.53876864 #0F0FFF
## 5 -2.53876864 -2.48357802 #1414FF
## 6 -2.48357802 -2.42838740 #1919FF
## 7 -2.42838740 -2.37319678 #1E1EFF
## 8 -2.37319678 -2.31800615 #2424FF
## 9 -2.31800615 -2.26281553 #2929FF
## 10 -2.26281553 -2.20762491 #2E2EFF
## 11 -2.20762491 -2.15243429 #3333FF
## 12 -2.15243429 -2.09724366 #3838FF
## 13 -2.09724366 -2.04205304 #3D3DFF
## 14 -2.04205304 -1.98686242 #4242FF
## 15 -1.98686242 -1.93167179 #4848FF
## 16 -1.93167179 -1.87648117 #4D4DFF
## 17 -1.87648117 -1.82129055 #5252FF
## 18 -1.82129055 -1.76609993 #5757FF
## 19 -1.76609993 -1.71090930 #5C5CFF
## 20 -1.71090930 -1.65571868 #6161FF
## 21 -1.65571868 -1.60052806 #6767FF
## 22 -1.60052806 -1.54533744 #6C6CFF
## 23 -1.54533744 -1.49014681 #7171FF
## 24 -1.49014681 -1.43495619 #7676FF
## 25 -1.43495619 -1.37976557 #7B7BFF
## 26 -1.37976557 -1.32457494 #8080FF
## 27 -1.32457494 -1.26938432 #8585FF
## 28 -1.26938432 -1.21419370 #8B8BFF
## 29 -1.21419370 -1.15900308 #9090FF
## 30 -1.15900308 -1.10381245 #9595FF
## 31 -1.10381245 -1.04862183 #9A9AFF
## 32 -1.04862183 -0.99343121 #9F9FFF
## 33 -0.99343121 -0.93824059 #A4A4FF
## 34 -0.93824059 -0.88304996 #AAAAFF
## 35 -0.88304996 -0.82785934 #AFAFFF
## 36 -0.82785934 -0.77266872 #B4B4FF
## 37 -0.77266872 -0.71747810 #B9B9FF
## 38 -0.71747810 -0.66228747 #BEBEFF
## 39 -0.66228747 -0.60709685 #C3C3FF
## 40 -0.60709685 -0.55190623 #C8C8FF
## 41 -0.55190623 -0.49671560 #CECEFF
## 42 -0.49671560 -0.44152498 #D3D3FF
## 43 -0.44152498 -0.38633436 #D8D8FF
## 44 -0.38633436 -0.33114374 #DDDDFF
## 45 -0.33114374 -0.27595311 #E2E2FF
## 46 -0.27595311 -0.22076249 #E7E7FF
## 47 -0.22076249 -0.16557187 #ECECFF
## 48 -0.16557187 -0.11038125 #F2F2FF
## 49 -0.11038125 -0.05519062 #F7F7FF
## 50 -0.05519062 0.00000000 #FCFCFF
## 51 0.00000000 0.05519062 #FFFCFC
## 52 0.05519062 0.11038125 #FFF7F7
## 53 0.11038125 0.16557187 #FFF2F2
## 54 0.16557187 0.22076249 #FFECEC
## 55 0.22076249 0.27595311 #FFE7E7
## 56 0.27595311 0.33114374 #FFE2E2
## 57 0.33114374 0.38633436 #FFDDDD
## 58 0.38633436 0.44152498 #FFD8D8
## 59 0.44152498 0.49671560 #FFD3D3
## 60 0.49671560 0.55190623 #FFCECE
## 61 0.55190623 0.60709685 #FFC8C8
## 62 0.60709685 0.66228747 #FFC3C3
## 63 0.66228747 0.71747810 #FFBEBE
## 64 0.71747810 0.77266872 #FFB9B9
## 65 0.77266872 0.82785934 #FFB4B4
## 66 0.82785934 0.88304996 #FFAFAF
## 67 0.88304996 0.93824059 #FFA9A9
## 68 0.93824059 0.99343121 #FFA4A4
## 69 0.99343121 1.04862183 #FF9F9F
## 70 1.04862183 1.10381245 #FF9A9A
## 71 1.10381245 1.15900308 #FF9595
## 72 1.15900308 1.21419370 #FF9090
## 73 1.21419370 1.26938432 #FF8B8B
## 74 1.26938432 1.32457494 #FF8585
## 75 1.32457494 1.37976557 #FF8080
## 76 1.37976557 1.43495619 #FF7B7B
## 77 1.43495619 1.49014681 #FF7676
## 78 1.49014681 1.54533744 #FF7171
## 79 1.54533744 1.60052806 #FF6C6C
## 80 1.60052806 1.65571868 #FF6767
## 81 1.65571868 1.71090930 #FF6161
## 82 1.71090930 1.76609993 #FF5C5C
## 83 1.76609993 1.82129055 #FF5757
## 84 1.82129055 1.87648117 #FF5252
## 85 1.87648117 1.93167179 #FF4D4D
## 86 1.93167179 1.98686242 #FF4848
## 87 1.98686242 2.04205304 #FF4242
## 88 2.04205304 2.09724366 #FF3D3D
## 89 2.09724366 2.15243429 #FF3838
## 90 2.15243429 2.20762491 #FF3333
## 91 2.20762491 2.26281553 #FF2E2E
## 92 2.26281553 2.31800615 #FF2929
## 93 2.31800615 2.37319678 #FF2424
## 94 2.37319678 2.42838740 #FF1E1E
## 95 2.42838740 2.48357802 #FF1919
## 96 2.48357802 2.53876864 #FF1414
## 97 2.53876864 2.59395927 #FF0F0F
## 98 2.59395927 2.64914989 #FF0A0A
## 99 2.64914989 2.70434051 #FF0505
## 100 2.70434051 2.75953113 #FF0000
##
## $`GO:0051726`$layout
## $`GO:0051726`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0051726`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0051726`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0009825`
## $`GO:0009825`$rowInd
## [1] 32 15 16 6 7 77 63 29 12 54 49 34 44 80 41 75 27 73 18 17 64 82 58 57 51
## [26] 65 61 13 28 59 81 38 74 72 76 37 71 78 43 3 46 83 42 5 52 22 10 36 48 24
## [51] 39 4 56 19 31 8 79 30 60 50 2 1 9 21 40 35 14 11 25 68 23 62 33 70 47
## [76] 45 26 67 53 66 55 20 69
##
## $`GO:0009825`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0009825`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0009825`$carpet
## AT2G20190 AT1G49040 AT1G58250 AT1G05850 AT1G10670
## P11554_207 -2.28218178 -1.4409725 -2.4283887 -1.43870549 -1.812601332
## P11554_208 -0.49514816 -0.4306467 0.7954388 -1.01068274 -1.076116866
## P11554_209 -0.56289907 0.7294349 0.8717575 -0.59211612 -0.612203857
## P11554_210 -0.87674593 -1.7465943 -0.7097829 -1.16912118 -0.508031951
## P11554_211 -0.85818751 -1.0136955 -1.4495324 -1.12533528 -0.531376678
## P11554_212 0.75521264 0.3299654 1.3607988 -0.85262580 -0.367493015
## P11554_213 -0.50789442 -0.1297716 -0.9272567 0.02438850 -0.716805151
## P11554_214 1.72630595 0.2392332 0.6829561 -0.07024538 -0.689297913
## P11554_215 1.00658737 -0.3815767 -0.7624221 -0.47341541 -0.701274708
## P11554_216 -0.33370851 -0.7128830 -0.4128755 0.00484085 0.006800093
## P11554_217 -0.24122932 0.5800763 1.3463368 -0.06538447 -0.047092829
## P11554_218 0.02664750 -0.7173010 -0.1192366 0.09336496 -0.018405471
## P11554_225 0.83491211 0.9149761 0.4814970 0.88418254 1.503063989
## P11554_226 1.16550623 1.5885562 0.5813550 1.89686568 1.491770599
## P11554_227 1.45674544 2.0338360 -0.2427777 1.82209087 1.848939835
## P11554_228 -0.73523928 -0.4733795 -0.2192989 0.01742714 0.202039977
## P11554_229 -0.11441205 0.8252470 0.5087664 1.29608567 1.119569667
## P11554_230 0.03572879 -0.1945045 0.6426650 0.75838566 0.908515611
## AT5G49720 AT5G01090 AT2G02130 AT1G23080 AT4G18710
## P11554_207 -0.6823674 -0.09015202 0.01713252 0.674748731 -1.216274915
## P11554_208 -0.9047459 0.32322628 0.05076319 0.426319350 -1.290426853
## P11554_209 -0.5661417 -0.32499450 -0.03928734 -0.691380173 -0.866838218
## P11554_210 -0.5465515 -1.02375119 -0.90925179 -0.012722497 0.834236455
## P11554_211 -0.5111637 -1.31942551 -0.93520142 -0.351838299 0.848678964
## P11554_212 -0.5312359 -0.55189534 -1.05071576 -0.597150415 0.849272907
## P11554_213 -0.5935653 -0.58046284 -0.37558268 -0.087036552 -1.239855103
## P11554_214 -0.7545226 -0.31657447 -0.34213695 -0.028887226 -1.606594544
## P11554_215 -0.7781193 -0.68043211 -0.43407410 -1.810929332 -1.364349410
## P11554_216 -0.6791795 -1.12356043 -1.13376506 0.192799452 0.429513460
## P11554_217 -0.5127397 -0.55572252 -1.14553558 0.052498066 0.192003268
## P11554_218 -0.5859705 -0.84741573 -1.18227594 0.001673925 0.613667344
## P11554_225 1.4951288 2.22686864 1.45984387 1.473101173 -0.002413995
## P11554_226 1.9789708 0.97273467 1.53401293 1.843796176 0.158985418
## P11554_227 2.0748340 1.70831161 1.53476641 1.707439114 0.165316518
## P11554_228 0.5691320 0.81107869 0.97305724 -0.588426362 0.853113798
## P11554_229 0.6930740 0.88103117 0.94000984 -0.463023393 1.564313074
## P11554_230 0.8351637 0.49113559 1.03824062 -1.740981738 1.077651833
## AT4G01710 AT2G35110 AT3G27000 AT5G64330 AT3G23050 AT5G28646
## P11554_207 -1.02457741 -1.12766340 -0.4279558 -0.74184868 -0.6671507 0.8393205
## P11554_208 -1.92764901 -0.92546091 -0.7990905 -0.42771097 -0.4122325 -1.1414701
## P11554_209 -0.31526634 -0.16136815 -0.9757085 -0.33287195 -0.5860213 -1.1414701
## P11554_210 1.19611385 1.16222671 0.1944211 0.29459574 0.5106285 1.1028001
## P11554_211 0.07998796 0.71551624 0.1515717 0.49176148 0.6011115 -1.1414701
## P11554_212 0.57737316 1.75834141 0.4177154 1.10910376 1.1684395 0.9238749
## P11554_213 -1.11210833 -1.88602659 -1.8489465 -1.60360225 -1.5226191 -1.1414701
## P11554_214 -0.87667361 -1.48077718 -1.0259444 -1.54885083 -1.0109060 0.3102521
## P11554_215 -1.61398917 -1.53036406 -1.5857696 -1.53866426 -2.0454680 -1.1414701
## P11554_216 0.51321881 0.19919032 0.1132091 -1.11962689 -0.6420635 0.3412774
## P11554_217 -0.07158179 0.39682708 0.1650685 -0.09277786 -0.4475978 -1.1414701
## P11554_218 0.48985680 0.34563823 0.2526989 -0.17602983 -0.4689222 0.2386424
## P11554_225 -0.39618910 0.36730541 0.4513085 0.98688077 0.4232849 1.4489162
## P11554_226 0.86065584 0.37626015 0.3950230 1.23913997 0.6429209 -1.1414701
## P11554_227 0.27863492 0.61785153 1.3064055 1.42560064 1.0390648 1.4215655
## P11554_228 1.26892759 -0.04805804 0.8403740 0.51737988 0.9715217 0.2214165
## P11554_229 0.53112965 0.41341391 2.2617883 0.70771404 1.4351375 0.6544848
## P11554_230 1.54213619 0.80714732 0.1138313 0.80980725 1.0108719 0.4877404
## AT1G80350 AT5G19530 AT1G69490 AT1G68530 AT5G05170
## P11554_207 -0.9210143 -0.2357023 -0.933121099 -1.2773911296 -1.97709478
## P11554_208 0.4173404 -0.2357023 -0.872664302 -1.1411272076 -1.62409129
## P11554_209 0.2060042 -0.2357023 -0.724020081 -1.2175560391 -1.34054902
## P11554_210 2.4492075 4.0069384 -0.311045068 -0.2245136358 0.31199408
## P11554_211 -0.6620706 -0.2357023 -0.130922974 -0.0008749247 -0.03145578
## P11554_212 -0.1809265 -0.2357023 -0.108150571 -0.0421397731 0.33925289
## P11554_213 -1.3557475 -0.2357023 -1.397445347 -1.0223561293 -0.57201339
## P11554_214 -1.1460196 -0.2357023 -0.878534598 -1.3009825678 -0.57303961
## P11554_215 0.5263613 -0.2357023 -0.941779697 -0.3481235187 -0.51729484
## P11554_216 0.1811567 -0.2357023 -0.008539624 1.0051780263 1.02016662
## P11554_217 -1.4076465 -0.2357023 0.186478653 0.8429466639 1.69703185
## P11554_218 0.5963907 -0.2357023 0.355065256 0.8449938383 1.60679581
## P11554_225 -0.8288288 -0.2357023 -0.085921076 0.0059472215 -0.22171608
## P11554_226 -0.5745994 -0.2357023 0.216734200 -0.3915162970 0.26960675
## P11554_227 1.4029087 -0.2357023 0.003104770 -0.2131078070 0.13047404
## P11554_228 0.1568745 -0.2357023 1.945053741 1.7929434057 0.25388050
## P11554_229 0.5127832 -0.2357023 1.445622511 1.0179811837 0.44091998
## P11554_230 0.6278260 -0.2357023 2.240085306 1.6696986903 0.78713228
## AT5G64740 AT4G32410 AT4G25570 AT4G03190 AT5G05690
## P11554_207 -2.014962e+00 -1.96913613 -0.84883168 -1.54199648 -0.5599841
## P11554_208 -1.359551e+00 -1.79301975 -0.71936723 -0.98771680 -0.4097569
## P11554_209 -1.837182e+00 -1.81509513 0.05851049 -0.75767772 -0.1061118
## P11554_210 -8.596158e-02 -0.20907940 0.13894337 1.05104985 0.9842324
## P11554_211 -3.567546e-05 -0.07905556 -0.02295902 1.26981383 0.6501148
## P11554_212 1.664214e-01 0.12949894 0.61441819 0.87812034 0.6044131
## P11554_213 -7.127469e-01 -0.33188830 -1.04066882 -0.97365817 -1.2572266
## P11554_214 -3.638990e-01 -0.31150590 -0.92656912 -0.24427344 -1.2331532
## P11554_215 -6.055002e-01 -0.50231428 -0.38573771 -0.99637785 -1.3686288
## P11554_216 1.153162e+00 0.55469477 1.44068492 1.56129308 0.9256641
## P11554_217 1.117372e+00 0.84259192 1.48855931 1.29446184 1.4520231
## P11554_218 4.630431e-01 0.76294832 2.24351207 1.13019023 1.1631404
## P11554_225 9.203314e-01 0.21825013 -1.63464700 -1.06269614 -1.5411179
## P11554_226 4.045431e-01 0.71543460 -0.41720025 -0.25094384 -0.3253863
## P11554_227 4.638969e-01 0.51031723 -0.14117964 -0.66939864 -1.1123328
## P11554_228 1.328551e+00 0.96165804 -0.62960716 0.02748101 0.8853658
## P11554_229 1.902588e-02 0.98304785 0.82572558 0.64365109 0.9212474
## P11554_230 9.434914e-01 1.33265267 -0.04358631 -0.37132218 0.3274971
## AT4G38430 AT1G28440 AT2G01420 AT4G33000 AT5G64340
## P11554_207 -1.558857610 0.97746540 0.15236853 0.6057781 -0.276784304
## P11554_208 -0.643273626 -0.35144929 -0.07299311 0.3065574 -1.443748422
## P11554_209 0.125525590 0.46695764 -0.37258835 -1.4519327 -1.237353139
## P11554_210 -0.014313620 0.70134344 0.88981697 0.6221513 1.391899234
## P11554_211 0.281295807 1.03980494 1.80615453 0.9722309 1.901066276
## P11554_212 0.610415792 0.91091508 0.76524454 0.8296339 1.429554727
## P11554_213 -1.056307610 -0.05974311 -0.78106972 -0.3150898 0.422574440
## P11554_214 -0.633685616 0.45172829 -0.85310448 -1.6571811 -0.732651443
## P11554_215 -2.190347716 -1.03812321 -0.73744403 -1.5958911 0.016139400
## P11554_216 1.098578204 1.26968910 1.31493490 0.9965131 0.905710797
## P11554_217 1.801970383 0.79678088 1.17415993 0.6173667 0.243995208
## P11554_218 1.032837526 0.70050691 0.48384647 1.3481437 -0.006127085
## P11554_225 0.088601558 -0.37559356 0.59175771 0.7853968 0.723668531
## P11554_226 0.007914576 -0.64782905 0.02222867 0.0725274 -0.478690853
## P11554_227 0.677634697 -1.73288865 -0.10847839 -0.7358714 -0.938841224
## P11554_228 0.058239274 0.25165721 -0.86031424 0.6369099 0.197950857
## P11554_229 0.973297431 -1.65560721 -1.84422703 -0.7171010 -0.742792035
## P11554_230 -0.659525041 -1.70561481 -1.57029289 -1.3201422 -1.375570965
## AT3G16370 AT5G25810 AT5G17690 AT5G35360 AT2G39900 AT5G16390
## P11554_207 1.0257705 0.5744941 -1.03529922 -0.3603583 0.1531087 -0.05529769
## P11554_208 -0.9104516 -0.6142808 0.08629735 0.6962365 0.7470900 0.57834057
## P11554_209 1.4069450 0.7157153 0.81795916 0.7571425 1.1293947 0.96426130
## P11554_210 -0.9104516 0.5860934 -0.23315873 -0.5399454 -0.3168960 -0.58414928
## P11554_211 0.3665829 -1.1543691 0.13917410 -0.8783955 -0.7568318 -0.66281860
## P11554_212 -0.9104516 0.7819146 0.28803620 -0.9079129 -0.2012845 -0.70341974
## P11554_213 -0.9104516 1.3201254 0.85257460 1.1982068 1.6424281 1.73218276
## P11554_214 1.0961653 1.3689348 0.15463817 2.2680933 1.6328567 1.40444278
## P11554_215 -0.9104516 -1.2427972 -2.47428659 1.5221335 1.0961000 1.73928315
## P11554_216 0.5389335 -0.1314794 0.01090603 -0.4135534 -0.1881365 0.17576184
## P11554_217 1.9043392 -0.5299937 0.89815655 0.1282068 0.3099101 0.15542037
## P11554_218 0.4386078 0.9021781 1.58050725 0.3926269 0.4415705 -0.27874247
## P11554_225 0.8803470 0.3059898 1.38816874 -0.3186570 -0.2664552 -0.30254969
## P11554_226 -0.9104516 -0.5111195 -0.03814341 0.1939218 -0.6535948 -0.09192852
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## P11554_229 -0.9104516 -2.0426386 -0.46475893 -0.5785580 -1.1432237 -1.25644653
## P11554_230 -0.9104516 -0.9543731 -0.29635725 -1.0391277 -1.0977185 -1.04691802
## AT5G55540 AT3G26520 AT1G04040 AT3G46550 AT5G65700
## P11554_207 0.45842811 0.23014574 0.69868343 0.89128591 0.545229250
## P11554_208 1.34242890 0.63017688 0.65342847 0.27778323 0.543852156
## P11554_209 0.83559809 0.90574984 0.67558289 0.07905788 -0.061085844
## P11554_210 -1.52150643 -1.07504471 -0.90059661 0.11268968 -0.387254030
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## P11554_213 1.50301863 1.68684336 1.38350656 1.44718296 1.664490404
## P11554_214 1.70967763 1.64047544 1.50421226 1.49474659 1.805586283
## P11554_215 1.32582354 0.82109642 1.57236454 1.16522141 0.742680387
## P11554_216 0.10373725 0.60115677 0.19373283 0.97871702 0.178367913
## P11554_217 -0.02560587 0.14242723 0.27976667 0.70251301 0.006242576
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## P11554_230 -0.82758167 -1.80427044 -1.59017531 -1.99052258 -2.014104540
## AT3G25500 AT1G04680 AT4G12420 AT1G75680 AT1G20330
## P11554_207 0.103237632 0.1305210 0.4206323 0.001797876 -0.037613419
## P11554_208 -0.021433789 0.1393429 0.4059979 -0.053148160 0.072492370
## P11554_209 -0.069116811 0.1162978 0.3106473 0.433190878 -0.001877165
## P11554_210 -0.004309135 -0.5718070 -0.5261248 -0.467226135 -0.416491999
## P11554_211 -0.124880399 -0.5539741 -0.5114943 -0.500872809 -0.314368630
## P11554_212 -0.108100016 -0.5566407 -0.4324348 -0.507387686 -0.734417179
## P11554_213 1.551500379 1.6795027 1.6442348 1.769265442 1.700101288
## P11554_214 1.385175987 1.5740844 1.6537383 1.850056452 1.283928358
## P11554_215 1.652816898 1.7061328 1.7463457 1.677400362 1.697073816
## P11554_216 0.869012687 0.6914776 0.5284163 0.380977956 0.933407517
## P11554_217 0.930364392 0.8112199 0.4965759 0.361631947 0.685152675
## P11554_218 0.512213085 0.8126033 0.4767656 0.606641794 0.983287363
## P11554_225 -0.657042935 -0.9888344 -0.9413676 -0.477236839 -0.492834676
## P11554_226 -0.917471296 -0.8922384 -0.8036239 -0.502628542 -0.626476482
## P11554_227 -1.030200670 -0.9145951 -0.9205760 -0.779850234 -0.929366085
## P11554_228 -1.037087097 -0.9693095 -1.1775179 -1.397980228 -1.218674281
## P11554_229 -1.540287288 -1.1007868 -1.0847362 -0.912493743 -1.032602120
## P11554_230 -1.494391624 -1.1129963 -1.2854785 -1.482138331 -1.550721353
## AT2G38120 AT3G54920 AT1G75780 AT3G18780 AT1G04430
## P11554_207 0.0394464878 -0.1002383 0.7535133 0.34721068 0.09369149
## P11554_208 0.0008088777 0.1686417 0.7876900 0.90393924 0.09799811
## P11554_209 0.4156624175 -0.0241720 0.8299920 0.92547420 0.12477088
## P11554_210 -0.6188198959 -0.4622545 -0.6759297 -0.19105964 -0.79691349
## P11554_211 -0.3959452715 -0.4673542 -0.5095886 0.02414633 -0.77831378
## P11554_212 -0.2351539872 -0.3677630 -0.2992172 -0.28823046 -0.47559532
## P11554_213 1.3588589121 1.4829512 1.4199078 1.27756931 1.83665848
## P11554_214 1.2629697932 1.4118994 1.3594669 1.38187080 1.69311865
## P11554_215 1.5599464210 1.5656610 1.1466363 1.51976546 1.99377540
## P11554_216 1.0086633279 0.9786680 0.7069129 0.25903341 0.06882908
## P11554_217 0.8592823538 1.1127158 0.4538419 0.32756349 0.19793365
## P11554_218 1.0676436220 0.8966971 0.3200301 0.44152921 0.40304813
## P11554_225 -1.0326034154 -0.9039239 -1.0627790 -1.34915980 -0.38620006
## P11554_226 -0.7439106568 -0.7700348 -0.4875277 -0.73250745 -0.12425794
## P11554_227 -0.7591355400 -0.9281876 -0.3711048 -0.94271219 -0.11703539
## P11554_228 -1.7244602130 -1.5157847 -1.6827823 -1.87117389 -1.32676721
## P11554_229 -0.7472180405 -0.9327575 -0.9101244 -0.85690584 -1.22007714
## P11554_230 -1.3160351926 -1.1447635 -1.7789375 -1.17635286 -1.28466354
## AT4G22010 AT1G70370 AT2G06850 AT1G13180 AT5G60920
## P11554_207 -0.1004695 0.1321233190 -0.28418932 -0.32819847 -0.67194342
## P11554_208 -0.3557234 0.0463369751 -0.02655698 -0.13117949 -0.76416858
## P11554_209 -0.3502187 0.0090923914 -0.17601287 -0.07189387 -0.32722227
## P11554_210 -0.5948613 -0.8219879616 -1.31683186 -1.93887820 -0.76678497
## P11554_211 -0.5364894 -0.5881166670 -1.25182637 -1.42291154 -0.87232119
## P11554_212 -0.5711944 -0.6473969795 -1.31223910 -1.23882381 -0.68294702
## P11554_213 1.9802822 2.0218741487 1.43012791 1.01662046 1.30515024
## P11554_214 1.9402287 2.0138477053 1.60786692 1.14425723 1.09195439
## P11554_215 2.0026420 2.0236322925 1.53054544 2.11697475 1.55173740
## P11554_216 0.3785924 -0.0134925836 0.87775225 0.66013620 0.18640108
## P11554_217 0.3836589 -0.0007030037 0.90492857 0.19445438 0.06438717
## P11554_218 0.3472979 0.1533455530 0.85858598 0.72196402 0.48496024
## P11554_225 -0.5436030 -0.5860777012 -0.12844153 -0.47124739 0.46897696
## P11554_226 -0.5975724 -0.4963712601 0.05377913 -0.74625648 1.54843541
## P11554_227 -0.5351365 -0.6304553438 -0.01169223 0.65750016 1.05026821
## P11554_228 -0.9048802 -0.8343048311 -0.92802097 -0.47670250 -1.38678177
## P11554_229 -0.8699981 -0.9510708155 -0.99679771 -0.19231427 -0.80752648
## P11554_230 -1.0725552 -0.8302752381 -0.83097726 0.50649880 -1.47257540
## AT2G03680 AT4G34490 AT4G02500 AT1G03060 AT1G01610
## P11554_207 -0.03054995 0.1576405 -0.42200558 -0.373849458 -0.33464569
## P11554_208 0.53077080 0.5046696 -0.17516191 -0.007727273 -0.30532881
## P11554_209 1.11361999 0.3029150 -0.30186229 -0.689497141 0.49463864
## P11554_210 -0.83760348 -1.4410397 -1.06517094 -1.313972982 -0.03463039
## P11554_211 -1.36049477 -1.4601673 -1.75731088 -0.017491051 0.17783810
## P11554_212 -0.86325799 -1.0189151 -1.52586382 0.318937269 -0.14233778
## P11554_213 0.77975799 1.2693461 1.43277002 -1.234734097 -0.43344970
## P11554_214 0.56061346 1.2528968 1.08768781 0.619754601 0.08675036
## P11554_215 0.56631863 1.3559358 1.03857551 2.089295842 1.19661033
## P11554_216 -0.17098674 -0.3813236 -0.58082434 1.159326467 1.68845265
## P11554_217 -0.85300731 -0.4497620 -0.65543088 2.131706252 1.81916667
## P11554_218 -0.48875702 -0.1477535 -0.40281928 0.105761537 1.29801207
## P11554_225 0.52481123 0.8761985 0.74712115 -0.845794862 -1.84699698
## P11554_226 1.61657790 1.0862091 1.94251131 -0.957614055 -1.32419917
## P11554_227 1.80662779 1.0057022 0.72669071 -0.239883943 -1.06588120
## P11554_228 -1.75601576 -1.2609505 -0.19703573 -0.829228451 -0.10002299
## P11554_229 -0.40122462 -0.6259879 0.03076861 0.012245535 -0.69780163
## P11554_230 -0.73720014 -1.0256140 0.07736055 0.072765810 -0.47617448
## AT1G20090 AT1G75500 AT3G19820 AT2G35620 AT1G31420
## P11554_207 -0.983719794 -0.3902587 -0.54533063 -0.55495962 -0.63914798
## P11554_208 -0.918627710 -0.2868709 -0.31151040 0.14223958 -0.45979071
## P11554_209 -0.659476038 -0.2257476 -0.01902099 -0.37271774 -0.25158051
## P11554_210 -0.737783294 -0.5722793 -0.21898309 -0.57288008 -0.17980932
## P11554_211 0.009207102 -0.7715492 -0.08166242 0.14354116 -0.09436904
## P11554_212 0.059048358 -0.4532669 -0.22749764 0.05080408 -0.35565893
## P11554_213 1.318783003 1.4466148 0.58341604 1.18474768 1.54754243
## P11554_214 0.953749615 1.4544411 0.65260557 1.26158757 1.03624783
## P11554_215 1.266885662 1.3546947 1.07389620 1.15230527 0.70991783
## P11554_216 1.535511254 1.3416080 1.47542973 1.17295103 1.76415529
## P11554_217 1.456091735 1.2437729 1.83873147 1.49467941 1.28186137
## P11554_218 1.303033001 1.0929334 1.54903489 1.03748104 0.61026981
## P11554_225 -0.696623841 -1.2169398 -1.03889363 -0.84517591 -0.19666369
## P11554_226 -1.000706175 -1.0947589 -0.62547497 -0.60963820 -0.12918129
## P11554_227 -0.470655839 -0.9605654 -0.45348122 -0.53251688 -0.49806389
## P11554_228 -0.607525813 -0.8580990 -1.68029178 -1.48131700 -0.60187145
## P11554_229 -0.792601888 -0.3876202 -0.68541741 -1.19259641 -1.54456132
## P11554_230 -1.034589339 -0.7161092 -1.28554971 -1.47853499 -1.99929644
## AT1G20340 AT1G75840 AT5G13140 AT1G75750 AT4G39400
## P11554_207 1.01644381 0.54694352 -1.26297727 -0.95375884 1.385782906
## P11554_208 1.45661734 0.45025982 -1.27697821 -0.51670471 1.131456424
## P11554_209 0.22632970 -0.75304842 -0.52706148 -1.02196971 0.958323074
## P11554_210 -0.05794997 0.29189740 -0.50095982 -0.65514389 -0.076478699
## P11554_211 -0.09428053 -0.72815192 -0.21136520 -0.76821814 0.310177409
## P11554_212 -0.38495847 -0.26485244 -1.01818255 -0.81158314 -0.167607977
## P11554_213 0.84235799 1.10655835 1.27879419 0.48207136 1.054076419
## P11554_214 0.72785802 1.05329683 0.53897804 0.58784168 1.788821503
## P11554_215 0.30960630 1.18271116 0.32249849 0.11469440 -0.091168748
## P11554_216 0.41275914 0.84567814 2.24534277 2.05027800 0.403506729
## P11554_217 1.03087469 1.16907449 0.28535322 1.77428864 -0.009908983
## P11554_218 1.41066395 0.99186040 0.87076374 1.74650183 -0.543731381
## P11554_225 -0.56947245 -0.84085844 -0.04046908 0.02415789 -0.184896670
## P11554_226 -1.34218368 -1.98862335 0.54930951 0.27570880 -0.976717812
## P11554_227 -1.26224848 -0.58047786 0.48550228 0.11929717 -1.286183995
## P11554_228 -1.73900921 0.06593904 -1.04337266 -0.70213291 -0.548636253
## P11554_229 -0.56446714 -0.95991485 0.74413081 -0.85172064 -1.771386981
## P11554_230 -1.41894101 -1.58829187 -1.43930677 -0.89360778 -1.375426965
## AT2G22230 AT5G16000 AT3G49670 AT3G28860 AT1G77690
## P11554_207 1.0627713 1.32218058 1.4360529 0.54681087 1.25858416
## P11554_208 1.3035155 1.15514663 1.0212062 1.80613819 1.29833018
## P11554_209 1.1822391 1.18460195 0.9937498 2.16661571 1.29806366
## P11554_210 -0.2938410 -0.50346485 -0.3790207 0.07153399 -0.08319365
## P11554_211 -0.6770948 -0.53808854 -0.3085628 -0.49101941 -0.44865092
## P11554_212 -0.6309863 -0.37373781 -0.5917863 -1.05085720 0.04604019
## P11554_213 1.2224555 1.47046117 1.5127321 0.71420168 1.41329883
## P11554_214 1.3060921 1.33880034 1.5467758 1.19823743 0.93459776
## P11554_215 1.3158271 1.01071823 1.0893604 0.54238190 0.91310351
## P11554_216 -0.2496589 0.01872454 -0.4058656 -0.25044487 -0.57331632
## P11554_217 -0.1034830 -0.18638494 0.1190370 -0.25845368 -1.38474177
## P11554_218 -0.2956307 -0.12433466 -0.6735481 -0.72762278 -0.20878277
## P11554_225 -0.5057470 -0.37063862 -0.5009542 -0.45836919 -0.46281390
## P11554_226 -0.1150234 -0.44738873 -0.8079379 -0.57264912 -0.35890205
## P11554_227 -0.1712178 -0.75997242 -0.2929350 -0.86536408 -0.57610251
## P11554_228 -1.7075093 -1.28621057 -1.0099797 -0.58891672 -0.70081258
## P11554_229 -1.1933839 -1.46148411 -1.2478727 -1.68900357 -2.15153189
## P11554_230 -1.4493246 -1.44892820 -1.5004512 -0.09321917 -0.21316992
## AT5G12250 AT4G16370 AT5G10480 AT4G20270 AT1G70940 AT5G15580
## P11554_207 1.01310448 1.3422224 1.5715760 1.5179526 1.0366200 1.02178742
## P11554_208 1.07728782 1.6146736 1.3639700 1.6981218 0.6948856 0.78256022
## P11554_209 1.74123425 1.9323134 1.0121945 1.3365347 0.6959209 -1.19950752
## P11554_210 -0.22340226 -0.8496640 -1.0062667 -0.1817974 -0.6718035 -1.19950752
## P11554_211 -0.05105366 -0.3137256 -0.8318559 -0.4130531 -0.6620231 0.49221522
## P11554_212 -0.15911724 -0.4179660 -1.5981943 -0.0108936 -0.6008609 0.13800552
## P11554_213 0.62819604 -0.1750249 1.0763069 0.4164654 0.5871451 2.03796579
## P11554_214 0.94442155 0.3432319 0.3090903 0.2807110 0.3735167 0.12988330
## P11554_215 0.34820451 0.1672251 1.0738117 -0.5662655 -0.1316799 0.16387542
## P11554_216 -0.23399446 -0.3770950 -0.3728101 -1.4086533 -1.1124177 -1.19950752
## P11554_217 -0.51877346 -0.7531351 -0.6060035 -1.5492392 -1.0332450 0.11941155
## P11554_218 -0.14546970 -0.8167276 -0.5070895 -1.1714298 -1.4056628 -1.19950752
## P11554_225 -0.22207016 0.2208150 0.4120355 1.0140866 1.6854588 1.17259628
## P11554_226 0.45539693 1.0219985 0.5006293 0.6478689 1.3605829 0.18013072
## P11554_227 0.40784419 0.7569491 0.6556301 0.6129272 1.4339803 -1.19950752
## P11554_228 -2.43063000 -1.3176311 -0.8887407 -0.6231104 -0.1813889 0.04853354
## P11554_229 -1.03457418 -0.9909587 -1.4240676 -0.8067912 -1.0761732 -1.19950752
## P11554_230 -1.59660466 -1.3875010 -0.7402163 -0.7934348 -0.9928553 0.91008012
##
## $`GO:0009825`$rowDendrogram
## 'dendrogram' with 2 branches and 83 members total, at height 3.456072
##
## $`GO:0009825`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0009825`$breaks
## [1] -4.00693843 -3.92679966 -3.84666089 -3.76652212 -3.68638335 -3.60624458
## [7] -3.52610582 -3.44596705 -3.36582828 -3.28568951 -3.20555074 -3.12541197
## [13] -3.04527320 -2.96513444 -2.88499567 -2.80485690 -2.72471813 -2.64457936
## [19] -2.56444059 -2.48430182 -2.40416306 -2.32402429 -2.24388552 -2.16374675
## [25] -2.08360798 -2.00346921 -1.92333044 -1.84319168 -1.76305291 -1.68291414
## [31] -1.60277537 -1.52263660 -1.44249783 -1.36235907 -1.28222030 -1.20208153
## [37] -1.12194276 -1.04180399 -0.96166522 -0.88152645 -0.80138769 -0.72124892
## [43] -0.64111015 -0.56097138 -0.48083261 -0.40069384 -0.32055507 -0.24041631
## [49] -0.16027754 -0.08013877 0.00000000 0.08013877 0.16027754 0.24041631
## [55] 0.32055507 0.40069384 0.48083261 0.56097138 0.64111015 0.72124892
## [61] 0.80138769 0.88152645 0.96166522 1.04180399 1.12194276 1.20208153
## [67] 1.28222030 1.36235907 1.44249783 1.52263660 1.60277537 1.68291414
## [73] 1.76305291 1.84319168 1.92333044 2.00346921 2.08360798 2.16374675
## [79] 2.24388552 2.32402429 2.40416306 2.48430182 2.56444059 2.64457936
## [85] 2.72471813 2.80485690 2.88499567 2.96513444 3.04527320 3.12541197
## [91] 3.20555074 3.28568951 3.36582828 3.44596705 3.52610582 3.60624458
## [97] 3.68638335 3.76652212 3.84666089 3.92679966 4.00693843
##
## $`GO:0009825`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0009825`$colorTable
## low high color
## 1 -4.00693843 -3.92679966 #0000FF
## 2 -3.92679966 -3.84666089 #0505FF
## 3 -3.84666089 -3.76652212 #0A0AFF
## 4 -3.76652212 -3.68638335 #0F0FFF
## 5 -3.68638335 -3.60624458 #1414FF
## 6 -3.60624458 -3.52610582 #1919FF
## 7 -3.52610582 -3.44596705 #1E1EFF
## 8 -3.44596705 -3.36582828 #2424FF
## 9 -3.36582828 -3.28568951 #2929FF
## 10 -3.28568951 -3.20555074 #2E2EFF
## 11 -3.20555074 -3.12541197 #3333FF
## 12 -3.12541197 -3.04527320 #3838FF
## 13 -3.04527320 -2.96513444 #3D3DFF
## 14 -2.96513444 -2.88499567 #4242FF
## 15 -2.88499567 -2.80485690 #4848FF
## 16 -2.80485690 -2.72471813 #4D4DFF
## 17 -2.72471813 -2.64457936 #5252FF
## 18 -2.64457936 -2.56444059 #5757FF
## 19 -2.56444059 -2.48430182 #5C5CFF
## 20 -2.48430182 -2.40416306 #6161FF
## 21 -2.40416306 -2.32402429 #6767FF
## 22 -2.32402429 -2.24388552 #6C6CFF
## 23 -2.24388552 -2.16374675 #7171FF
## 24 -2.16374675 -2.08360798 #7676FF
## 25 -2.08360798 -2.00346921 #7B7BFF
## 26 -2.00346921 -1.92333044 #8080FF
## 27 -1.92333044 -1.84319168 #8585FF
## 28 -1.84319168 -1.76305291 #8B8BFF
## 29 -1.76305291 -1.68291414 #9090FF
## 30 -1.68291414 -1.60277537 #9595FF
## 31 -1.60277537 -1.52263660 #9A9AFF
## 32 -1.52263660 -1.44249783 #9F9FFF
## 33 -1.44249783 -1.36235907 #A4A4FF
## 34 -1.36235907 -1.28222030 #AAAAFF
## 35 -1.28222030 -1.20208153 #AFAFFF
## 36 -1.20208153 -1.12194276 #B4B4FF
## 37 -1.12194276 -1.04180399 #B9B9FF
## 38 -1.04180399 -0.96166522 #BEBEFF
## 39 -0.96166522 -0.88152645 #C3C3FF
## 40 -0.88152645 -0.80138769 #C8C8FF
## 41 -0.80138769 -0.72124892 #CECEFF
## 42 -0.72124892 -0.64111015 #D3D3FF
## 43 -0.64111015 -0.56097138 #D8D8FF
## 44 -0.56097138 -0.48083261 #DDDDFF
## 45 -0.48083261 -0.40069384 #E2E2FF
## 46 -0.40069384 -0.32055507 #E7E7FF
## 47 -0.32055507 -0.24041631 #ECECFF
## 48 -0.24041631 -0.16027754 #F2F2FF
## 49 -0.16027754 -0.08013877 #F7F7FF
## 50 -0.08013877 0.00000000 #FCFCFF
## 51 0.00000000 0.08013877 #FFFCFC
## 52 0.08013877 0.16027754 #FFF7F7
## 53 0.16027754 0.24041631 #FFF2F2
## 54 0.24041631 0.32055507 #FFECEC
## 55 0.32055507 0.40069384 #FFE7E7
## 56 0.40069384 0.48083261 #FFE2E2
## 57 0.48083261 0.56097138 #FFDDDD
## 58 0.56097138 0.64111015 #FFD8D8
## 59 0.64111015 0.72124892 #FFD3D3
## 60 0.72124892 0.80138769 #FFCECE
## 61 0.80138769 0.88152645 #FFC8C8
## 62 0.88152645 0.96166522 #FFC3C3
## 63 0.96166522 1.04180399 #FFBEBE
## 64 1.04180399 1.12194276 #FFB9B9
## 65 1.12194276 1.20208153 #FFB4B4
## 66 1.20208153 1.28222030 #FFAFAF
## 67 1.28222030 1.36235907 #FFA9A9
## 68 1.36235907 1.44249783 #FFA4A4
## 69 1.44249783 1.52263660 #FF9F9F
## 70 1.52263660 1.60277537 #FF9A9A
## 71 1.60277537 1.68291414 #FF9595
## 72 1.68291414 1.76305291 #FF9090
## 73 1.76305291 1.84319168 #FF8B8B
## 74 1.84319168 1.92333044 #FF8585
## 75 1.92333044 2.00346921 #FF8080
## 76 2.00346921 2.08360798 #FF7B7B
## 77 2.08360798 2.16374675 #FF7676
## 78 2.16374675 2.24388552 #FF7171
## 79 2.24388552 2.32402429 #FF6C6C
## 80 2.32402429 2.40416306 #FF6767
## 81 2.40416306 2.48430182 #FF6161
## 82 2.48430182 2.56444059 #FF5C5C
## 83 2.56444059 2.64457936 #FF5757
## 84 2.64457936 2.72471813 #FF5252
## 85 2.72471813 2.80485690 #FF4D4D
## 86 2.80485690 2.88499567 #FF4848
## 87 2.88499567 2.96513444 #FF4242
## 88 2.96513444 3.04527320 #FF3D3D
## 89 3.04527320 3.12541197 #FF3838
## 90 3.12541197 3.20555074 #FF3333
## 91 3.20555074 3.28568951 #FF2E2E
## 92 3.28568951 3.36582828 #FF2929
## 93 3.36582828 3.44596705 #FF2424
## 94 3.44596705 3.52610582 #FF1E1E
## 95 3.52610582 3.60624458 #FF1919
## 96 3.60624458 3.68638335 #FF1414
## 97 3.68638335 3.76652212 #FF0F0F
## 98 3.76652212 3.84666089 #FF0A0A
## 99 3.84666089 3.92679966 #FF0505
## 100 3.92679966 4.00693843 #FF0000
##
## $`GO:0009825`$layout
## $`GO:0009825`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0009825`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0009825`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0048519`
## $`GO:0048519`$rowInd
## [1] 8 31 5 35 36 12 15 33 26 28 6 13 10 7 30 2 22 25 39 4 21 24 43 41 20
## [26] 18 42 38 19 27 16 37 3 44 1 17 32 46 9 14 23 11 40 29 34 45
##
## $`GO:0048519`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0048519`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0048519`$carpet
## AT1G52150 AT4G36260 AT1G19850 AT5G13300 AT5G25475
## P11554_207 0.156572852 -0.29479406 -1.92210941 -1.932065495 -1.6756594
## P11554_208 0.676954544 -0.57527208 -1.36846994 -1.068069619 -1.3156358
## P11554_209 0.008466485 -0.58433351 -0.73215680 -1.064417090 -1.5989665
## P11554_210 0.783778518 -0.08474480 0.78571471 -0.020603039 0.9298602
## P11554_211 -0.602879193 0.06675601 0.53335362 0.361416256 -0.0113235
## P11554_212 -0.178865691 -0.11015446 0.71795770 1.330457447 0.6815380
## P11554_213 -0.499098477 -1.56203200 0.26614883 -0.540481640 -0.1574369
## P11554_214 -0.161025108 -1.26404345 -0.07461912 -1.053435751 -1.4671597
## P11554_215 -1.690160563 -1.21625579 -0.66321046 -1.283056017 -0.5528083
## P11554_216 0.723860643 0.06939648 -0.43212757 0.301350938 0.9437296
## P11554_217 -0.992758887 0.14902350 0.10041533 1.878222099 0.6885873
## P11554_218 -0.201427481 0.46787861 -0.04367846 0.314316015 1.5370129
## P11554_225 -1.199809979 -0.78257035 -0.45574361 0.176382530 -0.6195375
## P11554_226 -1.257812386 0.29630969 -0.71027621 0.099686874 0.1498166
## P11554_227 -0.144536552 0.07636573 -0.70199737 1.079499443 0.6026779
## P11554_228 0.867014126 2.15570585 1.32800851 -0.007849787 0.5309910
## P11554_229 2.123158085 1.55171551 1.45399474 0.490880804 1.1273434
## P11554_230 1.588569062 1.64104914 1.91879550 0.937766033 0.2069706
## AT1G70510 AT1G79420 AT5G02030 AT3G43920 AT4G08150
## P11554_207 -1.01131630 -1.1028652 -0.6329378 -1.64727307 0.37590680
## P11554_208 -1.56447815 -1.1917885 -0.6179165 -0.91117855 -0.04447810
## P11554_209 -1.33033933 -1.0412391 -0.3524780 -0.42900811 -1.03632017
## P11554_210 0.88088994 0.1544668 1.1595349 0.61625960 1.11318062
## P11554_211 0.46887833 0.7710753 1.3132091 1.07774021 1.13983336
## P11554_212 1.62836124 0.4252904 1.1799659 1.04526891 1.96051502
## P11554_213 -1.01291010 -1.7736890 -1.8140522 -1.66881669 -1.31856193
## P11554_214 -0.74597588 -1.0421616 -1.6393306 -0.83540882 -1.11833320
## P11554_215 -1.53663203 -0.9829379 -1.4745319 -1.38626714 -1.91834763
## P11554_216 0.19304709 1.4363963 0.8264781 0.86854066 0.04212180
## P11554_217 0.32637763 0.8893524 0.7574347 1.58115735 -0.63823425
## P11554_218 1.36583023 0.7987895 0.5978811 0.90555754 -0.04605341
## P11554_225 -0.46303259 -0.1058179 -0.2084781 -0.12680717 -0.36267578
## P11554_226 0.58362602 -0.4813264 -0.4786688 -0.17036943 0.40792919
## P11554_227 0.03432441 0.1809118 -0.5550081 -0.30558078 -0.42609481
## P11554_228 0.64035419 1.2716288 0.5059021 -0.02024755 -0.04738538
## P11554_229 0.80902353 1.2762117 0.7481412 0.57803997 0.98078032
## P11554_230 0.73397176 0.5177025 0.6848550 0.82839307 0.93621757
## AT1G30330 AT1G73590 AT1G60860 AT1G48410 AT4G32551
## P11554_207 0.37934066 -0.1151538 -1.76418508 -1.52185850 -0.24586246
## P11554_208 -0.92726383 -0.2941705 1.04476694 0.05451137 -0.02343463
## P11554_209 -0.29809229 -0.3176070 -1.04317608 0.29427536 1.24411664
## P11554_210 0.13255580 -0.2657448 -1.52609755 -1.20210992 -1.44750996
## P11554_211 0.18115603 -0.3123709 -0.80043708 -1.01390535 -0.96563300
## P11554_212 -0.55767153 -0.3816624 0.04036054 -0.17301048 -1.40266329
## P11554_213 -0.10539620 -0.5371149 0.44329222 0.48140777 0.55744855
## P11554_214 0.86483836 -0.6531772 0.24602003 0.93994463 -0.33049464
## P11554_215 1.04995918 -1.0692602 -0.51819749 0.46290840 1.41713729
## P11554_216 0.15032905 -1.0119873 -1.12831809 0.73776929 0.60384180
## P11554_217 -0.91906143 -1.1585317 -0.63820830 1.72800670 -0.35985219
## P11554_218 -2.60235619 -1.3913922 -0.23912672 1.12843318 0.75311016
## P11554_225 1.23596415 1.7004744 0.65532742 -1.93815311 -1.04945055
## P11554_226 1.19254147 1.5557086 1.44164004 -0.82091856 1.10591582
## P11554_227 0.80507326 1.5832300 1.41305039 0.47505566 0.96265526
## P11554_228 0.75969663 1.1805458 0.74612759 -0.70839668 -1.78357653
## P11554_229 0.02562416 0.6931540 0.60332578 0.20531390 0.41395223
## P11554_230 -1.36723729 0.7950598 1.02383544 0.87072635 0.55029948
## AT1G05470 AT3G06220 AT3G28730 AT5G57130 AT1G19100
## P11554_207 -0.55064565 0.93786779 -0.13054870 1.4512796 0.85285717
## P11554_208 1.72393185 0.08097672 0.19426429 1.3523204 0.47615795
## P11554_209 1.11361441 0.35884004 1.06469143 1.1701421 1.52265480
## P11554_210 -0.51362135 -1.08909536 -0.55302107 0.3810231 -0.39598221
## P11554_211 -0.49112664 0.03867335 -0.77290097 0.6642141 -1.00829444
## P11554_212 -0.15962125 -0.56294562 0.52339236 0.5280195 -0.40876177
## P11554_213 1.50759782 0.17856303 1.15459167 0.3447799 0.90535078
## P11554_214 1.63213840 2.69080999 0.42138809 0.3718922 1.76569946
## P11554_215 0.39597610 0.82583363 1.57421692 -0.1040715 1.83300112
## P11554_216 -1.46001337 -1.20398077 -1.59885563 -1.2127096 -0.86905400
## P11554_217 -1.11057812 -0.09120888 -0.16269951 -1.1243942 0.14067567
## P11554_218 -1.58759547 -0.68813499 0.01480992 -1.1522168 -0.81039677
## P11554_225 0.29574658 -0.81967462 -1.77644692 0.9318380 -1.26379514
## P11554_226 -0.06072421 -0.49139023 -0.26071494 0.1330641 -0.82247029
## P11554_227 -0.70162298 -1.20686308 -0.90377567 0.2678905 -0.36477375
## P11554_228 -0.36971004 -0.71493122 -0.66735898 -1.2073352 -1.02865351
## P11554_229 -0.14696567 0.58602709 -0.01222251 -1.1007479 -0.42887911
## P11554_230 0.48321959 1.17063314 1.89119023 -1.6949882 -0.09533598
## AT2G47230 AT3G13510 AT5G62710 AT5G60690 AT2G44830
## P11554_207 1.1782779 1.30262488 1.5392857 0.609433897 0.80581378
## P11554_208 1.2746736 1.60711005 1.4319446 1.025417961 1.02486007
## P11554_209 1.1717015 1.22616731 1.2854779 0.726978046 1.29617783
## P11554_210 -0.6616361 -0.51955537 -0.3226055 -0.004920479 0.06069699
## P11554_211 -0.5155419 -0.37405312 -0.4641876 0.160288892 0.38397556
## P11554_212 -0.4668954 -0.25271378 -0.5979181 0.153122327 0.31616620
## P11554_213 1.5551862 1.28597982 1.2052610 1.106340436 0.93088919
## P11554_214 1.4495981 1.23821660 0.8791366 1.500158029 1.18714697
## P11554_215 1.4838396 0.90406443 1.4285698 1.261095041 0.95190328
## P11554_216 -0.4404988 -0.49121556 -0.6916353 0.097966305 -0.25297114
## P11554_217 -0.6088417 -0.27389849 -0.6113671 0.349407029 0.11301722
## P11554_218 -0.6391131 -0.07082667 -0.3887391 -0.066268727 -0.02924328
## P11554_225 -0.7398462 -0.45055733 -0.3014641 -0.856669791 -0.64414576
## P11554_226 -0.6015085 -0.61639476 -0.3008002 -0.575119201 -0.59438830
## P11554_227 -0.5664692 -0.48569855 -0.3771507 -0.497328347 -0.29637744
## P11554_228 -0.8885405 -1.52622514 -1.1322669 -1.907059087 -1.78316614
## P11554_229 -1.0595206 -0.98997895 -1.1437554 -1.320359655 -1.57373492
## P11554_230 -0.9248649 -1.51304536 -1.4377855 -1.762482677 -1.89662010
## AT2G27230 AT5G61480 AT5G43810 AT2G33860 AT3G54080
## P11554_207 0.92628602 0.71686773 1.078106753 0.64700594 0.8489459
## P11554_208 1.35114539 0.46995704 1.293367617 1.23322376 0.9817542
## P11554_209 1.43312539 1.66142938 1.637428463 1.63892601 0.7574954
## P11554_210 0.28348186 0.43833391 -0.571227883 0.11115952 -1.8740987
## P11554_211 -0.22404143 -0.05571976 -0.044726623 -1.42059070 -0.8502134
## P11554_212 -0.07059428 0.44007215 0.442939512 -0.18507643 -0.7913779
## P11554_213 1.30802503 0.79960120 0.482358113 0.55349080 1.1756606
## P11554_214 1.36107845 1.54255928 1.275407582 0.76647625 1.2606653
## P11554_215 0.24784792 0.85074852 0.265311577 1.18876297 0.5503506
## P11554_216 -0.51896222 0.71210071 -0.688008688 0.28865694 -0.2072481
## P11554_217 0.26457570 -0.05384457 -0.046085440 -0.15455706 -0.7834513
## P11554_218 -0.03906801 -0.58619764 -0.660969030 0.05143184 -0.7054176
## P11554_225 -1.25257556 -1.08093420 -0.738120266 -1.27813823 0.8755322
## P11554_226 -0.46037926 -0.73755952 0.559766566 0.46406547 0.7411367
## P11554_227 -0.33965069 -0.97987595 -0.002159109 -0.21091300 0.9279799
## P11554_228 -1.61709093 -1.21364127 -2.283075403 -1.87546219 -0.5504296
## P11554_229 -1.07136983 -1.23871281 -0.848652249 -0.26553596 -0.8678323
## P11554_230 -1.58183353 -1.68518422 -1.151661491 -1.55292592 -1.4894520
## AT1G79820 AT5G37020 AT1G12430 AT5G63950 AT1G04050
## P11554_207 0.1581543 1.4536112 1.130268852 0.24195515 -1.18808291
## P11554_208 0.7660900 0.7792609 1.042356049 1.75196736 1.52700572
## P11554_209 0.5101658 0.3462930 0.260588455 1.20202743 0.59337929
## P11554_210 -1.8000609 0.8672717 0.714572374 -0.08229845 0.06159009
## P11554_211 -0.9851449 1.6531233 0.718633594 0.41721309 0.33757959
## P11554_212 -0.4351422 0.7084768 0.937865146 0.08753884 -0.50320010
## P11554_213 1.3778828 0.1904828 0.706998070 0.42581077 1.41334991
## P11554_214 1.5969123 0.7414240 1.394024051 0.45992408 1.47239697
## P11554_215 1.3746959 0.3754656 0.610928719 1.05492810 0.74451062
## P11554_216 0.1143520 0.6061175 0.004454834 -0.12780162 0.25271306
## P11554_217 -0.4153295 -0.7515121 0.252169888 0.34619345 0.42780250
## P11554_218 -0.1791708 -0.6017411 -0.228815363 0.26118091 0.73666730
## P11554_225 0.4159793 -1.2555954 -1.313934120 -2.29152000 -1.04740623
## P11554_226 0.7456074 -1.9010650 -1.178717365 -1.81331732 -1.05056258
## P11554_227 0.3409419 -0.9515683 -1.047697886 -1.10107850 -0.87398787
## P11554_228 -1.0534296 -0.5127728 -1.120933628 -0.36245902 -1.22364533
## P11554_229 -1.3365306 -0.5087687 -1.213374567 -0.75237006 -1.59867099
## P11554_230 -1.1959730 -1.2385036 -1.669387104 0.28210578 -0.08143904
## AT2G16640 AT4G37750 AT5G67200 AT1G52310 AT1G78430 AT3G07540
## P11554_207 0.6681754 0.4504652 0.8784195 0.3347911 1.19798459 -0.04299732
## P11554_208 0.5569782 0.5426326 0.3959100 1.1593615 0.03525632 -0.05457814
## P11554_209 0.6902944 0.5738580 0.3482398 0.1920263 -0.17941563 -0.20560698
## P11554_210 0.1868968 -0.3228272 -0.2916372 -0.6373051 0.61274202 -0.06546332
## P11554_211 0.1319129 -0.3615204 -0.2556464 -0.2159094 0.06925074 -0.14112408
## P11554_212 0.1512288 -0.2609121 -0.4727112 -0.5807162 0.83672211 0.06244964
## P11554_213 1.4021818 1.5853454 1.6374005 1.0279786 0.38203448 0.93138757
## P11554_214 1.5143467 1.5893372 1.6339219 0.9177961 0.63825693 1.06159238
## P11554_215 1.0333479 1.6328643 1.6167500 1.4121368 0.65056031 0.86036085
## P11554_216 0.5251713 0.4239936 0.4518568 1.0206551 1.31271786 1.55579884
## P11554_217 0.3959585 0.4172873 0.3892172 1.2563267 1.17752343 1.52181309
## P11554_218 0.1679808 0.4468524 0.1388616 -0.1787383 0.68190954 1.24512635
## P11554_225 -0.9850780 -1.0237987 -0.8023481 -1.7476072 -0.80706366 -1.33200831
## P11554_226 -1.2216291 -1.1195121 -0.9328552 -0.2840614 -1.46256699 -1.31959155
## P11554_227 -1.4723522 -0.9051880 -0.9126182 -0.1504639 -1.31210509 -1.39645947
## P11554_228 -1.0680542 -1.2120945 -1.1655429 -1.7000081 -1.83971946 -0.86437454
## P11554_229 -1.8622212 -1.2689671 -1.3525274 -1.3909118 -1.08327738 -0.76494677
## P11554_230 -0.8151387 -1.1878159 -1.3046907 -0.4353509 -0.91081014 -1.05137822
## AT1G62360 AT5G58930 AT4G30520 AT5G03680 AT5G64340
## P11554_207 -0.28857348 -0.09739625 -1.23792720 1.10457886 -0.276784304
## P11554_208 -0.35359603 -0.40356086 0.19192144 0.17694678 -1.443748422
## P11554_209 -0.33118594 -0.40838801 0.11025213 -0.03162993 -1.237353139
## P11554_210 0.32907634 0.79781582 0.67224206 1.47718347 1.391899234
## P11554_211 0.36333371 0.57861525 1.67392327 1.14091819 1.901066276
## P11554_212 0.48448137 0.72045614 1.29726468 1.12533134 1.429554727
## P11554_213 0.08083966 -0.71569665 -0.69066438 -0.49061154 0.422574440
## P11554_214 0.35795627 -0.39813736 0.72838307 -0.01068629 -0.732651443
## P11554_215 0.25607036 0.11329756 -0.66149251 -0.71196905 0.016139400
## P11554_216 1.86336791 1.78416124 0.14370403 0.91594717 0.905710797
## P11554_217 1.62444078 1.95386522 0.45689574 0.93937172 0.243995208
## P11554_218 1.56010139 1.53063154 0.31787870 0.17893741 -0.006127085
## P11554_225 -1.66960119 -0.71242114 -0.34597774 0.32549123 0.723668531
## P11554_226 -0.83874105 -0.77394594 -0.75856714 -0.65110189 -0.478690853
## P11554_227 -0.99022961 -1.15859309 1.48977335 -0.88141211 -0.938841224
## P11554_228 -1.57618909 -1.01094230 -1.35248031 -1.81121245 0.197950857
## P11554_229 -0.18467809 -0.73734509 -0.04506474 -1.39292465 -0.742792035
## P11554_230 -0.68687331 -1.06241607 -1.99006447 -1.40315824 -1.375570965
##
## $`GO:0048519`$rowDendrogram
## 'dendrogram' with 2 branches and 46 members total, at height 2.597293
##
## $`GO:0048519`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0048519`$breaks
## [1] -2.6908100 -2.6369938 -2.5831776 -2.5293614 -2.4755452 -2.4217290
## [7] -2.3679128 -2.3140966 -2.2602804 -2.2064642 -2.1526480 -2.0988318
## [13] -2.0450156 -1.9911994 -1.9373832 -1.8835670 -1.8297508 -1.7759346
## [19] -1.7221184 -1.6683022 -1.6144860 -1.5606698 -1.5068536 -1.4530374
## [25] -1.3992212 -1.3454050 -1.2915888 -1.2377726 -1.1839564 -1.1301402
## [31] -1.0763240 -1.0225078 -0.9686916 -0.9148754 -0.8610592 -0.8072430
## [37] -0.7534268 -0.6996106 -0.6457944 -0.5919782 -0.5381620 -0.4843458
## [43] -0.4305296 -0.3767134 -0.3228972 -0.2690810 -0.2152648 -0.1614486
## [49] -0.1076324 -0.0538162 0.0000000 0.0538162 0.1076324 0.1614486
## [55] 0.2152648 0.2690810 0.3228972 0.3767134 0.4305296 0.4843458
## [61] 0.5381620 0.5919782 0.6457944 0.6996106 0.7534268 0.8072430
## [67] 0.8610592 0.9148754 0.9686916 1.0225078 1.0763240 1.1301402
## [73] 1.1839564 1.2377726 1.2915888 1.3454050 1.3992212 1.4530374
## [79] 1.5068536 1.5606698 1.6144860 1.6683022 1.7221184 1.7759346
## [85] 1.8297508 1.8835670 1.9373832 1.9911994 2.0450156 2.0988318
## [91] 2.1526480 2.2064642 2.2602804 2.3140966 2.3679128 2.4217290
## [97] 2.4755452 2.5293614 2.5831776 2.6369938 2.6908100
##
## $`GO:0048519`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0048519`$colorTable
## low high color
## 1 -2.6908100 -2.6369938 #0000FF
## 2 -2.6369938 -2.5831776 #0505FF
## 3 -2.5831776 -2.5293614 #0A0AFF
## 4 -2.5293614 -2.4755452 #0F0FFF
## 5 -2.4755452 -2.4217290 #1414FF
## 6 -2.4217290 -2.3679128 #1919FF
## 7 -2.3679128 -2.3140966 #1E1EFF
## 8 -2.3140966 -2.2602804 #2424FF
## 9 -2.2602804 -2.2064642 #2929FF
## 10 -2.2064642 -2.1526480 #2E2EFF
## 11 -2.1526480 -2.0988318 #3333FF
## 12 -2.0988318 -2.0450156 #3838FF
## 13 -2.0450156 -1.9911994 #3D3DFF
## 14 -1.9911994 -1.9373832 #4242FF
## 15 -1.9373832 -1.8835670 #4848FF
## 16 -1.8835670 -1.8297508 #4D4DFF
## 17 -1.8297508 -1.7759346 #5252FF
## 18 -1.7759346 -1.7221184 #5757FF
## 19 -1.7221184 -1.6683022 #5C5CFF
## 20 -1.6683022 -1.6144860 #6161FF
## 21 -1.6144860 -1.5606698 #6767FF
## 22 -1.5606698 -1.5068536 #6C6CFF
## 23 -1.5068536 -1.4530374 #7171FF
## 24 -1.4530374 -1.3992212 #7676FF
## 25 -1.3992212 -1.3454050 #7B7BFF
## 26 -1.3454050 -1.2915888 #8080FF
## 27 -1.2915888 -1.2377726 #8585FF
## 28 -1.2377726 -1.1839564 #8B8BFF
## 29 -1.1839564 -1.1301402 #9090FF
## 30 -1.1301402 -1.0763240 #9595FF
## 31 -1.0763240 -1.0225078 #9A9AFF
## 32 -1.0225078 -0.9686916 #9F9FFF
## 33 -0.9686916 -0.9148754 #A4A4FF
## 34 -0.9148754 -0.8610592 #AAAAFF
## 35 -0.8610592 -0.8072430 #AFAFFF
## 36 -0.8072430 -0.7534268 #B4B4FF
## 37 -0.7534268 -0.6996106 #B9B9FF
## 38 -0.6996106 -0.6457944 #BEBEFF
## 39 -0.6457944 -0.5919782 #C3C3FF
## 40 -0.5919782 -0.5381620 #C8C8FF
## 41 -0.5381620 -0.4843458 #CECEFF
## 42 -0.4843458 -0.4305296 #D3D3FF
## 43 -0.4305296 -0.3767134 #D8D8FF
## 44 -0.3767134 -0.3228972 #DDDDFF
## 45 -0.3228972 -0.2690810 #E2E2FF
## 46 -0.2690810 -0.2152648 #E7E7FF
## 47 -0.2152648 -0.1614486 #ECECFF
## 48 -0.1614486 -0.1076324 #F2F2FF
## 49 -0.1076324 -0.0538162 #F7F7FF
## 50 -0.0538162 0.0000000 #FCFCFF
## 51 0.0000000 0.0538162 #FFFCFC
## 52 0.0538162 0.1076324 #FFF7F7
## 53 0.1076324 0.1614486 #FFF2F2
## 54 0.1614486 0.2152648 #FFECEC
## 55 0.2152648 0.2690810 #FFE7E7
## 56 0.2690810 0.3228972 #FFE2E2
## 57 0.3228972 0.3767134 #FFDDDD
## 58 0.3767134 0.4305296 #FFD8D8
## 59 0.4305296 0.4843458 #FFD3D3
## 60 0.4843458 0.5381620 #FFCECE
## 61 0.5381620 0.5919782 #FFC8C8
## 62 0.5919782 0.6457944 #FFC3C3
## 63 0.6457944 0.6996106 #FFBEBE
## 64 0.6996106 0.7534268 #FFB9B9
## 65 0.7534268 0.8072430 #FFB4B4
## 66 0.8072430 0.8610592 #FFAFAF
## 67 0.8610592 0.9148754 #FFA9A9
## 68 0.9148754 0.9686916 #FFA4A4
## 69 0.9686916 1.0225078 #FF9F9F
## 70 1.0225078 1.0763240 #FF9A9A
## 71 1.0763240 1.1301402 #FF9595
## 72 1.1301402 1.1839564 #FF9090
## 73 1.1839564 1.2377726 #FF8B8B
## 74 1.2377726 1.2915888 #FF8585
## 75 1.2915888 1.3454050 #FF8080
## 76 1.3454050 1.3992212 #FF7B7B
## 77 1.3992212 1.4530374 #FF7676
## 78 1.4530374 1.5068536 #FF7171
## 79 1.5068536 1.5606698 #FF6C6C
## 80 1.5606698 1.6144860 #FF6767
## 81 1.6144860 1.6683022 #FF6161
## 82 1.6683022 1.7221184 #FF5C5C
## 83 1.7221184 1.7759346 #FF5757
## 84 1.7759346 1.8297508 #FF5252
## 85 1.8297508 1.8835670 #FF4D4D
## 86 1.8835670 1.9373832 #FF4848
## 87 1.9373832 1.9911994 #FF4242
## 88 1.9911994 2.0450156 #FF3D3D
## 89 2.0450156 2.0988318 #FF3838
## 90 2.0988318 2.1526480 #FF3333
## 91 2.1526480 2.2064642 #FF2E2E
## 92 2.2064642 2.2602804 #FF2929
## 93 2.2602804 2.3140966 #FF2424
## 94 2.3140966 2.3679128 #FF1E1E
## 95 2.3679128 2.4217290 #FF1919
## 96 2.4217290 2.4755452 #FF1414
## 97 2.4755452 2.5293614 #FF0F0F
## 98 2.5293614 2.5831776 #FF0A0A
## 99 2.5831776 2.6369938 #FF0505
## 100 2.6369938 2.6908100 #FF0000
##
## $`GO:0048519`$layout
## $`GO:0048519`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0048519`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0048519`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0016458`
## $`GO:0016458`$rowInd
## [1] 27 48 46 19 57 38 47 32 7 54 29 3 8 52 49 6 2 9 40 39 30 18 12 25 10
## [26] 35 41 15 36 11 21 53 17 4 23 26 16 56 22 14 28 51 33 58 42 20 45 13 50 34
## [51] 37 55 44 43 5 1 31 24
##
## $`GO:0016458`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0016458`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0016458`$carpet
## AT3G02470 AT5G15510 AT5G14620 AT2G22610 AT5G63110
## P11554_207 -1.05119951 -0.008810111 -1.4402367 -1.36745670 -1.1813311
## P11554_208 -0.87172398 0.137158802 -1.1381411 -0.87677558 -1.1124271
## P11554_209 -0.29645663 0.358734496 -1.7750591 -0.95925543 -0.4600816
## P11554_210 1.30431898 1.628832850 0.6241171 1.02236520 0.8593594
## P11554_211 1.47336629 0.616464286 0.5823754 0.65782655 0.1622171
## P11554_212 1.70406847 2.282115087 1.1252871 0.87951265 0.6936841
## P11554_213 0.22533705 -1.652713659 -1.0014063 -1.89890622 -0.2689967
## P11554_214 0.03590086 -0.750123637 -0.6184812 -0.98418924 -2.0700372
## P11554_215 -0.46155720 -1.707972606 -1.0889238 -1.29070094 -1.7986601
## P11554_216 -0.13366946 -1.117242626 -0.2393719 0.88051902 0.8790115
## P11554_217 0.06326516 0.251549599 0.2906166 1.34237928 0.9552237
## P11554_218 0.14713438 -0.180107582 1.2218766 0.83517277 1.1195221
## P11554_225 -1.18312449 0.099012948 1.8081848 -0.24961633 -0.3811741
## P11554_226 -1.45423299 -0.687654629 0.2052824 0.29259658 0.6799717
## P11554_227 -1.46592682 -0.093377073 0.7190811 0.01107019 0.4225871
## P11554_228 0.76722824 -0.029175231 0.2504544 0.44533115 1.2489370
## P11554_229 1.30353940 0.110688578 -0.1334735 0.11327936 0.1395636
## P11554_230 -0.10626777 0.742620508 0.6078181 1.14684768 0.1126307
## AT4G11130 AT5G15380 AT3G23890 AT1G44110 AT5G55520
## P11554_207 -1.20817116 0.203458684 0.4747263 0.93283443 1.1708965
## P11554_208 -0.29313899 0.436918257 1.2923942 1.35918495 0.5590836
## P11554_209 -0.80268859 0.699101380 0.9777198 1.05602781 0.9127344
## P11554_210 0.26695250 0.015095822 0.4539379 0.62617353 0.5372966
## P11554_211 0.59170956 -0.958582919 0.1975577 0.42756483 0.1777599
## P11554_212 1.09483597 0.310937072 0.4311020 0.32853271 0.5738915
## P11554_213 -1.60393167 0.007447376 0.6447525 0.47831372 0.4235760
## P11554_214 -1.22732848 0.698405854 1.1789711 1.07093151 1.2030406
## P11554_215 -1.92313413 -0.129202752 0.6397487 0.46625017 0.4634155
## P11554_216 0.07155204 0.350749612 0.6002678 0.70911173 0.6705350
## P11554_217 -0.01775822 0.674685835 0.6567489 0.15044727 0.4995766
## P11554_218 -0.22752745 0.549861653 0.3635734 0.09817155 0.7051998
## P11554_225 0.46684278 -2.314936075 -1.4533920 -1.02018349 -1.0957572
## P11554_226 0.71905725 0.812217995 -1.4584113 -1.56596547 -1.2795542
## P11554_227 0.54404742 1.446889949 -1.0705713 -0.97802545 -1.5928805
## P11554_228 1.34182452 0.135355873 -1.2887196 -1.55503602 -1.3120804
## P11554_229 1.31423443 -2.314936075 -1.4728318 -1.01909161 -0.9373455
## P11554_230 0.89262221 -0.623467542 -1.1675742 -1.56524216 -1.6793882
## AT3G14190 AT1G05440 AT1G50240 AT5G49020 AT5G37010
## P11554_207 1.19637262 0.6913499 -0.08751811 0.1083347 0.72078871
## P11554_208 1.31651840 1.0107677 0.64935806 0.1937203 1.04372553
## P11554_209 0.91568087 1.4406834 0.68484050 0.4239454 -0.18762944
## P11554_210 0.78317796 0.9525019 0.11043846 0.2607693 0.99665889
## P11554_211 0.73935087 0.5252172 0.40245607 0.6001044 0.46034421
## P11554_212 0.80548209 -0.1010815 0.37674859 0.6130614 1.05882153
## P11554_213 0.72966616 1.3052538 0.76813298 0.2755085 0.27104474
## P11554_214 0.50166650 0.2793860 0.85666416 1.2198504 0.64354392
## P11554_215 -0.39429283 0.2978220 0.77533929 1.1080049 0.06643999
## P11554_216 0.40058689 0.2821980 1.08648986 1.0982299 0.93683936
## P11554_217 0.08980679 0.5395334 0.96786955 0.7538363 0.67130308
## P11554_218 0.25444068 0.2336478 0.94345103 0.8301483 0.91376449
## P11554_225 -1.46293034 -0.9852936 -1.96266255 -2.1559805 -1.37497204
## P11554_226 -1.58069430 -1.4383497 -1.63877405 -1.4052181 -1.52708912
## P11554_227 -1.06738510 -1.0729914 -1.04281336 -0.8471498 -1.10098078
## P11554_228 -1.49152379 -0.9503456 -1.29195009 -1.4025120 -1.07326932
## P11554_229 -0.36500120 -1.8992611 -0.42350696 -0.8695165 -0.70554546
## P11554_230 -1.37092228 -1.1110385 -1.17456343 -0.8051370 -1.81378831
## AT1G34355 AT1G03780 AT1G53140 AT4G22860 AT4G20910
## P11554_207 0.24804861 0.53760813 0.39175714 0.769142076 0.2286444
## P11554_208 0.41249520 0.75933169 0.78179429 0.691982764 0.9364704
## P11554_209 -0.01991303 0.81923249 0.43484096 0.125140231 0.7384526
## P11554_210 0.64174815 0.03242994 0.22532923 -0.004603819 -1.1259642
## P11554_211 0.48999551 0.39711162 -0.00813146 0.341413634 -0.6422914
## P11554_212 0.92099743 0.75816240 0.95345150 0.888930613 -0.5604655
## P11554_213 0.95520235 0.85744856 1.11920677 1.070392409 1.2835512
## P11554_214 0.45922760 0.66439273 1.06008994 0.871442902 0.7781553
## P11554_215 0.69784078 0.98226037 0.45497863 1.263928526 0.9060881
## P11554_216 1.36247064 0.93583105 1.00133897 0.615895371 -1.6546271
## P11554_217 0.91982736 0.71227313 1.01435747 0.840128593 -1.4122696
## P11554_218 0.69497838 0.56033352 0.21395967 0.166336455 -1.4278292
## P11554_225 -1.05633582 -1.25754505 -1.36682438 -1.409570459 0.8962905
## P11554_226 -1.72969005 -1.39697666 -1.14082651 -1.133563311 0.9466315
## P11554_227 -1.32848374 -1.01536198 -0.99607502 -1.274756717 0.9394540
## P11554_228 -1.35965654 -1.40545682 -1.59591057 -1.791297051 0.4817486
## P11554_229 -0.94739114 -1.35447664 -0.78051764 -0.681037560 -0.7306285
## P11554_230 -1.36136171 -1.58659848 -1.76281900 -1.349904656 -0.5814111
## AT3G20260 AT2G07170 AT1G63640 AT2G36200 AT1G59540
## P11554_207 1.356989112 1.16246877 0.65362148 0.789928494 0.89838602
## P11554_208 0.450287346 1.21521868 1.19793097 1.147157823 0.90761152
## P11554_209 0.298735970 1.21044060 0.66940459 1.240633443 0.85293264
## P11554_210 -0.056798598 -0.66107760 0.03018073 -0.023104453 -0.21382820
## P11554_211 -0.228332034 -0.12282299 0.11017199 -0.068006674 -0.18095297
## P11554_212 0.164737388 0.10803380 0.41654947 -0.008155888 0.13412257
## P11554_213 1.092446644 0.86065807 1.36595007 1.286910857 1.09666630
## P11554_214 1.339114000 1.47539009 1.35216418 1.451908875 1.77799150
## P11554_215 1.933467847 1.28567065 1.42003958 1.477508447 0.92163613
## P11554_216 0.304804141 -0.12647254 -0.05780029 -0.450342300 0.63155658
## P11554_217 0.008421198 0.05602871 -0.33709362 -0.267145883 0.33528696
## P11554_218 -0.164368265 0.23599004 0.21448053 -0.051833089 -0.06332676
## P11554_225 -0.622980957 -1.08364674 -1.16443712 -1.305396182 -1.31176673
## P11554_226 -1.373246245 -1.05232203 -1.22178465 -1.301268083 -0.83269463
## P11554_227 -1.113826203 -1.13010657 -1.55998944 -1.127871684 -1.43072396
## P11554_228 -1.034404668 -1.31162882 -1.35670972 -1.059346613 -1.52820159
## P11554_229 -0.638317165 -1.24453093 -0.81421892 -0.846733569 -0.87351120
## P11554_230 -1.716729512 -0.87729120 -0.91845984 -0.884843523 -1.12118416
## AT3G44050 AT4G26760 AT1G72250 AT3G51290 AT1G63470
## P11554_207 0.49062690 0.49237815 0.42812565 0.7964021 0.39827854
## P11554_208 1.44409164 1.02412101 1.44250027 0.5880725 0.72631587
## P11554_209 0.91545785 0.99777421 1.55304695 0.5335597 0.78423093
## P11554_210 -0.18305242 -0.22102436 -0.09069569 -0.1891357 -0.89809460
## P11554_211 -0.06699018 0.51842659 -0.38790248 0.2865837 -0.86570646
## P11554_212 0.31037187 -0.02816597 0.74583226 -0.1605962 -0.23404125
## P11554_213 1.41877855 1.11003081 0.40512159 1.3796540 1.12779060
## P11554_214 1.38927405 1.73901972 0.75619977 2.4027910 1.45144030
## P11554_215 0.92845116 1.21610106 0.76009427 0.7243514 2.39794751
## P11554_216 -0.23321926 -0.67844688 0.35010657 -0.2606224 -0.05419263
## P11554_217 0.14388483 -0.16629505 0.32174792 -0.3599353 -0.08785984
## P11554_218 0.04572015 -0.07629223 0.65321710 -0.6509858 -0.13224827
## P11554_225 -0.59927425 -0.61236862 -0.49392693 -1.1450880 -0.60672659
## P11554_226 -1.19753963 -1.10117486 -0.92000145 -0.7236093 0.15292517
## P11554_227 -0.65550479 -0.75218325 -0.82299784 -0.4278338 -0.92178326
## P11554_228 -1.91806737 -2.31365568 -2.03087407 -0.5410209 -1.38938201
## P11554_229 -1.57705282 -0.58290669 -1.64056304 -0.1462212 -0.76576286
## P11554_230 -0.65595628 -0.56533796 -1.02903083 -2.1063658 -1.08313112
## AT2G27040 AT5G49160 AT2G01120 AT1G08130 AT2G31650 AT2G42120
## P11554_207 0.41763475 1.16458835 1.3673048 1.0704173 0.9828711 0.9923037
## P11554_208 0.80432846 1.33503206 1.1245187 1.1235339 1.2924367 1.4416298
## P11554_209 0.97810208 1.33869939 1.3054209 1.4451343 1.4791522 1.4332230
## P11554_210 -0.80293132 -0.89386386 -0.6195260 -0.6183257 -0.9227062 -0.1428372
## P11554_211 -0.64779678 -0.83606417 -0.7211546 -0.4854937 -0.3913605 -0.3603117
## P11554_212 -0.42616786 -0.81260899 -0.1387222 -0.4523754 -0.6331581 -0.4765925
## P11554_213 1.79610316 1.31897871 1.3720305 1.3467417 1.4200196 1.0734640
## P11554_214 1.49547662 1.40369442 1.4692400 1.4970461 1.2678466 0.9746974
## P11554_215 1.67298644 1.36143996 1.4273952 1.5858800 1.6092564 1.7990594
## P11554_216 -0.33735093 -0.97870971 -0.8347709 -0.8514475 -0.9042858 -0.8005728
## P11554_217 0.24673487 -0.98081851 -0.8541389 -0.8167845 -0.7721309 -0.1910451
## P11554_218 -0.07633598 -0.89684827 -0.5658507 -0.7682538 -0.7183550 -0.8727801
## P11554_225 -0.57290586 -0.15778068 -0.9684401 -0.7710146 -0.6499586 -0.7574585
## P11554_226 -0.37937398 -0.09579880 -0.4686177 -0.3396039 -0.3604688 -0.3602489
## P11554_227 -0.36750535 -0.09725883 -0.5927264 -0.4455129 -0.3056104 -0.3393199
## P11554_228 -1.17399648 -0.78394688 -1.0442281 -0.6249507 -0.7020533 -1.2666587
## P11554_229 -1.09200549 -0.71419694 -0.7369275 -1.0783912 -1.0152369 -1.0887502
## P11554_230 -1.53499634 -0.67453726 -0.5208069 -0.8165994 -0.6762583 -1.0578018
## AT1G78770 AT5G62410 AT2G31270 AT1G69770 AT3G06930 AT5G48600
## P11554_207 1.0911893 0.9984663 1.3302474 1.2168231 1.0361988 1.1850839
## P11554_208 1.3025314 1.1344067 1.1977920 1.1287121 1.0531032 1.4112412
## P11554_209 1.3054000 1.2260337 1.0730228 1.1008244 1.1196234 1.2979243
## P11554_210 -0.3948275 -0.5818279 -0.3970551 -0.4566175 -0.4899215 -0.4601231
## P11554_211 -0.4746138 -0.4330440 -0.4924679 -0.5338723 -0.5805870 -0.5431664
## P11554_212 -0.4556716 -0.3687862 -0.3826736 -0.5311471 -0.4381157 -0.3626244
## P11554_213 1.1728965 1.1374980 1.4371205 1.5417596 1.5013435 1.3788438
## P11554_214 1.4445825 1.6968836 1.4683452 1.5372370 1.5409616 1.3865620
## P11554_215 1.6174674 1.6769697 1.5002337 1.5402341 1.5979495 1.4561109
## P11554_216 -0.7129891 -0.7732624 -0.4672640 -0.4820198 -0.3310363 -0.6694035
## P11554_217 -0.4645472 -0.1240111 -0.6042890 -0.5217882 -0.4974818 -0.5402411
## P11554_218 -0.4224507 -0.3218926 -0.5407428 -0.5244628 -0.3211456 -0.5947747
## P11554_225 -1.3014420 -0.7931206 -0.5467487 -0.6429901 -0.5331245 -0.8902324
## P11554_226 -0.4293049 -0.6897992 -0.6233182 -0.6681518 -0.5116349 -0.6540643
## P11554_227 -0.4588290 -0.6167416 -0.6736884 -0.6942066 -0.5610192 -0.5556733
## P11554_228 -1.1003175 -1.0435267 -1.0264521 -0.9726310 -1.1989506 -1.0114518
## P11554_229 -1.0351118 -1.1572843 -1.2234305 -1.0494889 -1.2535412 -0.9858013
## P11554_230 -0.6839622 -0.9669614 -1.0286311 -0.9882142 -1.1326217 -0.8482098
## AT3G24495 AT5G63960 AT4G30860 AT2G24490 AT5G08020 AT1G67630
## P11554_207 1.1759085 1.1713245 1.2598948 1.3906610 1.3098072 1.2757878
## P11554_208 1.3129506 1.4549063 1.2403666 1.2687255 1.2122490 1.4147095
## P11554_209 1.3620853 1.2718754 1.3010537 1.2807546 1.2485153 1.4695292
## P11554_210 -0.5086609 -0.4380328 -0.6242655 -0.5998294 -0.6317226 -0.5756564
## P11554_211 -0.5744437 -0.3767061 -0.6209217 -0.5995103 -0.5633658 -0.5893138
## P11554_212 -0.3793020 -0.1143842 -0.5137401 -0.5244005 -0.5783329 -0.5027818
## P11554_213 1.4568398 1.3679954 1.4751910 1.3542183 1.3925527 1.3049248
## P11554_214 1.3683543 1.3458729 1.3536179 1.3539319 1.4851550 1.3345465
## P11554_215 1.4233484 1.3777394 1.4328099 1.4659468 1.4855806 1.3331947
## P11554_216 -0.4544018 -0.7198209 -0.7992458 -0.6457795 -0.5645983 -0.6739194
## P11554_217 -0.6087522 -0.6517789 -0.6683867 -0.4058549 -0.6002815 -0.6655967
## P11554_218 -0.5533049 -0.5775556 -0.3873341 -0.4858176 -0.5847791 -0.6449196
## P11554_225 -0.7099810 -0.8001198 -0.6189537 -0.6618007 -0.4472875 -0.5866447
## P11554_226 -0.6408921 -0.7574147 -0.4748843 -0.5631934 -0.5694748 -0.4694051
## P11554_227 -0.6273739 -0.4070590 -0.2779060 -0.6241822 -0.6568106 -0.4650593
## P11554_228 -0.9496034 -1.1241694 -1.0382718 -0.9212376 -0.9987128 -0.9482895
## P11554_229 -1.0748779 -1.0238247 -0.9835280 -0.9274583 -0.9780567 -1.0463365
## P11554_230 -1.0178932 -0.9988476 -1.0554962 -1.1551737 -0.9604372 -0.9647698
## AT5G46280 AT3G42660 AT3G56870 AT5G58130 AT4G39630 AT4G33400
## P11554_207 1.2840035 1.2026529 1.0857548 1.4331919 1.02647377 1.0377675
## P11554_208 1.4012114 1.3543728 1.2818245 0.9594619 1.30862283 1.3307120
## P11554_209 1.3744306 1.3296797 1.0363244 0.7339383 0.83845930 0.6999784
## P11554_210 -0.6071882 -0.5845479 -0.5998170 -0.6547731 -0.79199267 -0.6473562
## P11554_211 -0.5419400 -0.5147894 -0.5952130 -0.7782167 -0.74361044 -0.5105969
## P11554_212 -0.5738425 -0.4083394 -0.4732082 -0.7555671 -0.46455499 -0.3410567
## P11554_213 1.2893939 1.3344438 1.6817398 1.6484543 1.57109110 1.7688255
## P11554_214 1.3415019 1.3634470 1.5408901 1.6000720 1.48010081 1.6508338
## P11554_215 1.4349610 1.4178038 1.4512960 1.6259530 1.55162575 1.3147365
## P11554_216 -0.4993116 -0.6261368 -0.8063276 -0.7142931 -0.20646988 -0.3756472
## P11554_217 -0.5836650 -0.4915054 -0.4851773 -0.5365953 -0.11366298 -0.1402530
## P11554_218 -0.6696976 -0.5518063 -0.7737659 -0.5813396 -0.07837407 -0.3951485
## P11554_225 -0.5530158 -0.4524528 -0.4604306 -0.3192966 -0.74846427 -1.1358228
## P11554_226 -0.5130034 -0.4968942 -0.6266917 -0.6935828 -0.70785048 -0.8962147
## P11554_227 -0.5526989 -0.4386445 -0.6421350 -0.8417391 -0.73462818 -0.7408285
## P11554_228 -0.9780033 -1.0858299 -0.6901882 -0.6302850 -0.94580201 -0.9997533
## P11554_229 -1.0929475 -1.1435044 -1.0785735 -0.6550591 -1.11229676 -0.7306821
## P11554_230 -0.9601884 -1.2079490 -0.8463015 -0.8403239 -1.12866685 -0.8894938
## AT1G09450 AT1G01370 AT3G22780 AT2G32590
## P11554_207 1.14067060 1.0774924 0.5648621 0.9158040
## P11554_208 1.01761081 0.9760469 0.5787601 1.1134653
## P11554_209 0.45465578 1.3844050 1.3331534 1.2933929
## P11554_210 -0.89141769 -0.2086459 -0.2123467 -0.7870728
## P11554_211 -0.09576789 -0.5515003 -0.5302097 -0.1643060
## P11554_212 -0.22788708 -0.5661568 -0.3613878 -0.2244563
## P11554_213 1.65709160 1.6468283 1.3574660 1.4311164
## P11554_214 1.79001639 1.1982197 1.5148655 1.1000030
## P11554_215 1.55472045 1.6721586 2.0534306 1.7474341
## P11554_216 -0.31097454 -0.5492081 -0.2543973 -0.3377033
## P11554_217 -0.65062580 -0.4413494 -0.2292852 -0.5916351
## P11554_218 -0.34015336 -0.5609742 -0.2746607 -0.1548873
## P11554_225 -0.63725106 -0.8324846 -0.8399609 -1.3558185
## P11554_226 -1.21314308 -0.9305390 -0.8689236 -0.9238693
## P11554_227 -0.76254832 -0.5722250 -0.5007497 -0.6470324
## P11554_228 -0.91513172 -1.1861148 -1.4326832 -1.4871688
## P11554_229 -0.59930136 -0.6316731 -0.9439907 -0.4577732
## P11554_230 -0.97056373 -0.9242798 -0.9539423 -0.4694927
##
## $`GO:0016458`$rowDendrogram
## 'dendrogram' with 2 branches and 58 members total, at height 2.475988
##
## $`GO:0016458`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0016458`$breaks
## [1] -2.40279104 -2.35473522 -2.30667940 -2.25862357 -2.21056775 -2.16251193
## [7] -2.11445611 -2.06640029 -2.01834447 -1.97028865 -1.92223283 -1.87417701
## [13] -1.82612119 -1.77806537 -1.73000955 -1.68195373 -1.63389790 -1.58584208
## [19] -1.53778626 -1.48973044 -1.44167462 -1.39361880 -1.34556298 -1.29750716
## [25] -1.24945134 -1.20139552 -1.15333970 -1.10528388 -1.05722806 -1.00917224
## [31] -0.96111641 -0.91306059 -0.86500477 -0.81694895 -0.76889313 -0.72083731
## [37] -0.67278149 -0.62472567 -0.57666985 -0.52861403 -0.48055821 -0.43250239
## [43] -0.38444657 -0.33639075 -0.28833492 -0.24027910 -0.19222328 -0.14416746
## [49] -0.09611164 -0.04805582 0.00000000 0.04805582 0.09611164 0.14416746
## [55] 0.19222328 0.24027910 0.28833492 0.33639075 0.38444657 0.43250239
## [61] 0.48055821 0.52861403 0.57666985 0.62472567 0.67278149 0.72083731
## [67] 0.76889313 0.81694895 0.86500477 0.91306059 0.96111641 1.00917224
## [73] 1.05722806 1.10528388 1.15333970 1.20139552 1.24945134 1.29750716
## [79] 1.34556298 1.39361880 1.44167462 1.48973044 1.53778626 1.58584208
## [85] 1.63389790 1.68195373 1.73000955 1.77806537 1.82612119 1.87417701
## [91] 1.92223283 1.97028865 2.01834447 2.06640029 2.11445611 2.16251193
## [97] 2.21056775 2.25862357 2.30667940 2.35473522 2.40279104
##
## $`GO:0016458`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0016458`$colorTable
## low high color
## 1 -2.40279104 -2.35473522 #0000FF
## 2 -2.35473522 -2.30667940 #0505FF
## 3 -2.30667940 -2.25862357 #0A0AFF
## 4 -2.25862357 -2.21056775 #0F0FFF
## 5 -2.21056775 -2.16251193 #1414FF
## 6 -2.16251193 -2.11445611 #1919FF
## 7 -2.11445611 -2.06640029 #1E1EFF
## 8 -2.06640029 -2.01834447 #2424FF
## 9 -2.01834447 -1.97028865 #2929FF
## 10 -1.97028865 -1.92223283 #2E2EFF
## 11 -1.92223283 -1.87417701 #3333FF
## 12 -1.87417701 -1.82612119 #3838FF
## 13 -1.82612119 -1.77806537 #3D3DFF
## 14 -1.77806537 -1.73000955 #4242FF
## 15 -1.73000955 -1.68195373 #4848FF
## 16 -1.68195373 -1.63389790 #4D4DFF
## 17 -1.63389790 -1.58584208 #5252FF
## 18 -1.58584208 -1.53778626 #5757FF
## 19 -1.53778626 -1.48973044 #5C5CFF
## 20 -1.48973044 -1.44167462 #6161FF
## 21 -1.44167462 -1.39361880 #6767FF
## 22 -1.39361880 -1.34556298 #6C6CFF
## 23 -1.34556298 -1.29750716 #7171FF
## 24 -1.29750716 -1.24945134 #7676FF
## 25 -1.24945134 -1.20139552 #7B7BFF
## 26 -1.20139552 -1.15333970 #8080FF
## 27 -1.15333970 -1.10528388 #8585FF
## 28 -1.10528388 -1.05722806 #8B8BFF
## 29 -1.05722806 -1.00917224 #9090FF
## 30 -1.00917224 -0.96111641 #9595FF
## 31 -0.96111641 -0.91306059 #9A9AFF
## 32 -0.91306059 -0.86500477 #9F9FFF
## 33 -0.86500477 -0.81694895 #A4A4FF
## 34 -0.81694895 -0.76889313 #AAAAFF
## 35 -0.76889313 -0.72083731 #AFAFFF
## 36 -0.72083731 -0.67278149 #B4B4FF
## 37 -0.67278149 -0.62472567 #B9B9FF
## 38 -0.62472567 -0.57666985 #BEBEFF
## 39 -0.57666985 -0.52861403 #C3C3FF
## 40 -0.52861403 -0.48055821 #C8C8FF
## 41 -0.48055821 -0.43250239 #CECEFF
## 42 -0.43250239 -0.38444657 #D3D3FF
## 43 -0.38444657 -0.33639075 #D8D8FF
## 44 -0.33639075 -0.28833492 #DDDDFF
## 45 -0.28833492 -0.24027910 #E2E2FF
## 46 -0.24027910 -0.19222328 #E7E7FF
## 47 -0.19222328 -0.14416746 #ECECFF
## 48 -0.14416746 -0.09611164 #F2F2FF
## 49 -0.09611164 -0.04805582 #F7F7FF
## 50 -0.04805582 0.00000000 #FCFCFF
## 51 0.00000000 0.04805582 #FFFCFC
## 52 0.04805582 0.09611164 #FFF7F7
## 53 0.09611164 0.14416746 #FFF2F2
## 54 0.14416746 0.19222328 #FFECEC
## 55 0.19222328 0.24027910 #FFE7E7
## 56 0.24027910 0.28833492 #FFE2E2
## 57 0.28833492 0.33639075 #FFDDDD
## 58 0.33639075 0.38444657 #FFD8D8
## 59 0.38444657 0.43250239 #FFD3D3
## 60 0.43250239 0.48055821 #FFCECE
## 61 0.48055821 0.52861403 #FFC8C8
## 62 0.52861403 0.57666985 #FFC3C3
## 63 0.57666985 0.62472567 #FFBEBE
## 64 0.62472567 0.67278149 #FFB9B9
## 65 0.67278149 0.72083731 #FFB4B4
## 66 0.72083731 0.76889313 #FFAFAF
## 67 0.76889313 0.81694895 #FFA9A9
## 68 0.81694895 0.86500477 #FFA4A4
## 69 0.86500477 0.91306059 #FF9F9F
## 70 0.91306059 0.96111641 #FF9A9A
## 71 0.96111641 1.00917224 #FF9595
## 72 1.00917224 1.05722806 #FF9090
## 73 1.05722806 1.10528388 #FF8B8B
## 74 1.10528388 1.15333970 #FF8585
## 75 1.15333970 1.20139552 #FF8080
## 76 1.20139552 1.24945134 #FF7B7B
## 77 1.24945134 1.29750716 #FF7676
## 78 1.29750716 1.34556298 #FF7171
## 79 1.34556298 1.39361880 #FF6C6C
## 80 1.39361880 1.44167462 #FF6767
## 81 1.44167462 1.48973044 #FF6161
## 82 1.48973044 1.53778626 #FF5C5C
## 83 1.53778626 1.58584208 #FF5757
## 84 1.58584208 1.63389790 #FF5252
## 85 1.63389790 1.68195373 #FF4D4D
## 86 1.68195373 1.73000955 #FF4848
## 87 1.73000955 1.77806537 #FF4242
## 88 1.77806537 1.82612119 #FF3D3D
## 89 1.82612119 1.87417701 #FF3838
## 90 1.87417701 1.92223283 #FF3333
## 91 1.92223283 1.97028865 #FF2E2E
## 92 1.97028865 2.01834447 #FF2929
## 93 2.01834447 2.06640029 #FF2424
## 94 2.06640029 2.11445611 #FF1E1E
## 95 2.11445611 2.16251193 #FF1919
## 96 2.16251193 2.21056775 #FF1414
## 97 2.21056775 2.25862357 #FF0F0F
## 98 2.25862357 2.30667940 #FF0A0A
## 99 2.30667940 2.35473522 #FF0505
## 100 2.35473522 2.40279104 #FF0000
##
## $`GO:0016458`$layout
## $`GO:0016458`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0016458`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0016458`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0010608`
## $`GO:0010608`$rowInd
## [1] 1 2
##
## $`GO:0010608`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0010608`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0010608`$carpet
## AT4G08980 AT4G21320
## P11554_207 -0.75660003 -0.45300927
## P11554_208 -0.68255147 -0.17878025
## P11554_209 -1.02410016 -0.59781456
## P11554_210 0.94244160 -0.51658085
## P11554_211 0.75798528 -0.84925185
## P11554_212 0.02061941 -0.92612083
## P11554_213 -1.42390879 -0.16905352
## P11554_214 -1.61572126 -0.33599388
## P11554_215 -1.63855666 -1.00565228
## P11554_216 0.28437632 -0.34833703
## P11554_217 0.13118648 -1.13647494
## P11554_218 0.01221541 -0.43813691
## P11554_225 0.97611498 1.67838792
## P11554_226 0.53815502 2.56647892
## P11554_227 0.21688168 1.04267927
## P11554_228 1.97309219 0.88941729
## P11554_229 0.73384262 0.05965655
## P11554_230 0.55452739 0.71858623
##
## $`GO:0010608`$rowDendrogram
## 'dendrogram' with 2 branches and 2 members total, at height 0.2780001
##
## $`GO:0010608`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0010608`$breaks
## [1] -2.56647892 -2.51514934 -2.46381977 -2.41249019 -2.36116061 -2.30983103
## [7] -2.25850145 -2.20717187 -2.15584229 -2.10451272 -2.05318314 -2.00185356
## [13] -1.95052398 -1.89919440 -1.84786482 -1.79653525 -1.74520567 -1.69387609
## [19] -1.64254651 -1.59121693 -1.53988735 -1.48855777 -1.43722820 -1.38589862
## [25] -1.33456904 -1.28323946 -1.23190988 -1.18058030 -1.12925073 -1.07792115
## [31] -1.02659157 -0.97526199 -0.92393241 -0.87260283 -0.82127326 -0.76994368
## [37] -0.71861410 -0.66728452 -0.61595494 -0.56462536 -0.51329578 -0.46196621
## [43] -0.41063663 -0.35930705 -0.30797747 -0.25664789 -0.20531831 -0.15398874
## [49] -0.10265916 -0.05132958 0.00000000 0.05132958 0.10265916 0.15398874
## [55] 0.20531831 0.25664789 0.30797747 0.35930705 0.41063663 0.46196621
## [61] 0.51329578 0.56462536 0.61595494 0.66728452 0.71861410 0.76994368
## [67] 0.82127326 0.87260283 0.92393241 0.97526199 1.02659157 1.07792115
## [73] 1.12925073 1.18058030 1.23190988 1.28323946 1.33456904 1.38589862
## [79] 1.43722820 1.48855777 1.53988735 1.59121693 1.64254651 1.69387609
## [85] 1.74520567 1.79653525 1.84786482 1.89919440 1.95052398 2.00185356
## [91] 2.05318314 2.10451272 2.15584229 2.20717187 2.25850145 2.30983103
## [97] 2.36116061 2.41249019 2.46381977 2.51514934 2.56647892
##
## $`GO:0010608`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0010608`$colorTable
## low high color
## 1 -2.56647892 -2.51514934 #0000FF
## 2 -2.51514934 -2.46381977 #0505FF
## 3 -2.46381977 -2.41249019 #0A0AFF
## 4 -2.41249019 -2.36116061 #0F0FFF
## 5 -2.36116061 -2.30983103 #1414FF
## 6 -2.30983103 -2.25850145 #1919FF
## 7 -2.25850145 -2.20717187 #1E1EFF
## 8 -2.20717187 -2.15584229 #2424FF
## 9 -2.15584229 -2.10451272 #2929FF
## 10 -2.10451272 -2.05318314 #2E2EFF
## 11 -2.05318314 -2.00185356 #3333FF
## 12 -2.00185356 -1.95052398 #3838FF
## 13 -1.95052398 -1.89919440 #3D3DFF
## 14 -1.89919440 -1.84786482 #4242FF
## 15 -1.84786482 -1.79653525 #4848FF
## 16 -1.79653525 -1.74520567 #4D4DFF
## 17 -1.74520567 -1.69387609 #5252FF
## 18 -1.69387609 -1.64254651 #5757FF
## 19 -1.64254651 -1.59121693 #5C5CFF
## 20 -1.59121693 -1.53988735 #6161FF
## 21 -1.53988735 -1.48855777 #6767FF
## 22 -1.48855777 -1.43722820 #6C6CFF
## 23 -1.43722820 -1.38589862 #7171FF
## 24 -1.38589862 -1.33456904 #7676FF
## 25 -1.33456904 -1.28323946 #7B7BFF
## 26 -1.28323946 -1.23190988 #8080FF
## 27 -1.23190988 -1.18058030 #8585FF
## 28 -1.18058030 -1.12925073 #8B8BFF
## 29 -1.12925073 -1.07792115 #9090FF
## 30 -1.07792115 -1.02659157 #9595FF
## 31 -1.02659157 -0.97526199 #9A9AFF
## 32 -0.97526199 -0.92393241 #9F9FFF
## 33 -0.92393241 -0.87260283 #A4A4FF
## 34 -0.87260283 -0.82127326 #AAAAFF
## 35 -0.82127326 -0.76994368 #AFAFFF
## 36 -0.76994368 -0.71861410 #B4B4FF
## 37 -0.71861410 -0.66728452 #B9B9FF
## 38 -0.66728452 -0.61595494 #BEBEFF
## 39 -0.61595494 -0.56462536 #C3C3FF
## 40 -0.56462536 -0.51329578 #C8C8FF
## 41 -0.51329578 -0.46196621 #CECEFF
## 42 -0.46196621 -0.41063663 #D3D3FF
## 43 -0.41063663 -0.35930705 #D8D8FF
## 44 -0.35930705 -0.30797747 #DDDDFF
## 45 -0.30797747 -0.25664789 #E2E2FF
## 46 -0.25664789 -0.20531831 #E7E7FF
## 47 -0.20531831 -0.15398874 #ECECFF
## 48 -0.15398874 -0.10265916 #F2F2FF
## 49 -0.10265916 -0.05132958 #F7F7FF
## 50 -0.05132958 0.00000000 #FCFCFF
## 51 0.00000000 0.05132958 #FFFCFC
## 52 0.05132958 0.10265916 #FFF7F7
## 53 0.10265916 0.15398874 #FFF2F2
## 54 0.15398874 0.20531831 #FFECEC
## 55 0.20531831 0.25664789 #FFE7E7
## 56 0.25664789 0.30797747 #FFE2E2
## 57 0.30797747 0.35930705 #FFDDDD
## 58 0.35930705 0.41063663 #FFD8D8
## 59 0.41063663 0.46196621 #FFD3D3
## 60 0.46196621 0.51329578 #FFCECE
## 61 0.51329578 0.56462536 #FFC8C8
## 62 0.56462536 0.61595494 #FFC3C3
## 63 0.61595494 0.66728452 #FFBEBE
## 64 0.66728452 0.71861410 #FFB9B9
## 65 0.71861410 0.76994368 #FFB4B4
## 66 0.76994368 0.82127326 #FFAFAF
## 67 0.82127326 0.87260283 #FFA9A9
## 68 0.87260283 0.92393241 #FFA4A4
## 69 0.92393241 0.97526199 #FF9F9F
## 70 0.97526199 1.02659157 #FF9A9A
## 71 1.02659157 1.07792115 #FF9595
## 72 1.07792115 1.12925073 #FF9090
## 73 1.12925073 1.18058030 #FF8B8B
## 74 1.18058030 1.23190988 #FF8585
## 75 1.23190988 1.28323946 #FF8080
## 76 1.28323946 1.33456904 #FF7B7B
## 77 1.33456904 1.38589862 #FF7676
## 78 1.38589862 1.43722820 #FF7171
## 79 1.43722820 1.48855777 #FF6C6C
## 80 1.48855777 1.53988735 #FF6767
## 81 1.53988735 1.59121693 #FF6161
## 82 1.59121693 1.64254651 #FF5C5C
## 83 1.64254651 1.69387609 #FF5757
## 84 1.69387609 1.74520567 #FF5252
## 85 1.74520567 1.79653525 #FF4D4D
## 86 1.79653525 1.84786482 #FF4848
## 87 1.84786482 1.89919440 #FF4242
## 88 1.89919440 1.95052398 #FF3D3D
## 89 1.95052398 2.00185356 #FF3838
## 90 2.00185356 2.05318314 #FF3333
## 91 2.05318314 2.10451272 #FF2E2E
## 92 2.10451272 2.15584229 #FF2929
## 93 2.15584229 2.20717187 #FF2424
## 94 2.20717187 2.25850145 #FF1E1E
## 95 2.25850145 2.30983103 #FF1919
## 96 2.30983103 2.36116061 #FF1414
## 97 2.36116061 2.41249019 #FF0F0F
## 98 2.41249019 2.46381977 #FF0A0A
## 99 2.46381977 2.51514934 #FF0505
## 100 2.51514934 2.56647892 #FF0000
##
## $`GO:0010608`$layout
## $`GO:0010608`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0010608`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0010608`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0007059`
## $`GO:0007059`$rowInd
## [1] 11 33 32 6 20 2 26 17 21 9 40 39 36 3 23 14 19 22 15 5 12 1 24 27 13
## [26] 25 42 35 4 30 8 18 31 37 41 16 29 38 7 28 10 34
##
## $`GO:0007059`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0007059`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0007059`$carpet
## AT2G32900 AT5G12260 AT5G08450 AT1G70510 AT3G47950
## P11554_207 -1.19693166 -1.54004627 -1.47962192 -1.01131630 -1.169284615
## P11554_208 -1.75391100 -1.28788054 -0.89919221 -1.56447815 -0.692490694
## P11554_209 -0.66119402 -1.54623420 -1.04902843 -1.33033933 -0.278356343
## P11554_210 -0.39900824 0.11900228 -0.39162610 0.88088994 -0.222741195
## P11554_211 0.49172827 -0.44283925 0.07653797 0.46887833 0.205568854
## P11554_212 0.10613364 -0.09774761 0.75662635 1.62836124 -0.009028352
## P11554_213 -0.33035726 -1.11539059 -0.73175110 -1.01291010 -0.382855823
## P11554_214 -0.80127861 0.44547319 -0.32950300 -0.74597588 -2.423957257
## P11554_215 0.40001860 0.18290228 -0.34526474 -1.53663203 -1.256759313
## P11554_216 0.19268910 -0.43714300 0.87604753 0.19304709 0.515203128
## P11554_217 -1.01882587 0.70088444 1.19934628 0.32637763 0.013799432
## P11554_218 -0.52090315 -0.39219730 0.71174786 1.36583023 0.365041023
## P11554_225 1.46649391 1.87788020 -0.98492518 -0.46303259 0.048194653
## P11554_226 1.97454087 1.16128174 0.51807011 0.58362602 0.222725026
## P11554_227 1.75295303 1.16250474 -0.61932480 0.03432441 1.550669160
## P11554_228 0.07774632 0.84151787 -0.74475484 0.64035419 1.286945200
## P11554_229 0.45027569 -0.53865544 1.16494518 0.80902353 0.672019922
## P11554_230 -0.23016962 0.90668747 2.27167104 0.73397176 1.555307195
## AT1G63990 AT4G16440 AT3G13170 AT3G48190 AT2G03430 AT5G61460
## P11554_207 -1.0819733 0.9109396 0.8452952 -1.77477657 -0.64387454 0.1690030
## P11554_208 1.5028218 1.0012075 0.9286599 -0.21023818 0.76057955 0.5745332
## P11554_209 -0.2122820 0.1954302 0.5583977 1.00886386 1.08338791 0.4296886
## P11554_210 0.7888017 -2.2096651 -1.0124865 -0.90368515 -0.58271925 -1.1566688
## P11554_211 1.0662396 -1.1421248 -1.1203453 -1.31731613 -0.44720304 -1.3100682
## P11554_212 0.5564114 -0.9835008 -0.5345785 0.16135563 -1.01665127 -0.9219234
## P11554_213 -0.8173164 -0.3500896 -0.1577089 -0.73511169 -0.19880019 0.1434596
## P11554_214 -0.8484475 0.2892436 0.7883983 -0.15680781 0.04166522 0.3320849
## P11554_215 -0.1849842 1.6423301 1.1567461 -0.16563591 -0.64706158 0.2835217
## P11554_216 0.2448448 -0.4663315 -1.2434783 -1.18961856 -1.70223351 -1.6677165
## P11554_217 0.9731614 -0.2039709 -1.7331162 -0.46042218 -1.20536341 -1.4624459
## P11554_218 0.4966269 -0.4977975 -1.1619559 -0.06536888 -1.26267499 -1.2568870
## P11554_225 -2.5365512 -0.9868317 1.2562533 0.40073269 0.35384292 0.9054863
## P11554_226 -0.5970184 0.3090278 0.4033785 0.76311391 1.77737545 1.0073601
## P11554_227 1.2066453 -0.3289292 1.2755456 2.12908261 1.06493726 1.0946348
## P11554_228 -0.2449562 0.2420137 -0.8290287 0.60035603 0.77131047 0.8349256
## P11554_229 0.3056214 1.2504948 0.7575585 0.45008873 0.67743293 0.7664692
## P11554_230 -0.6176448 1.3285538 -0.1775347 1.46538761 1.17605008 1.2345427
## AT5G60110 AT5G18950 AT1G67420 AT3G54670 AT3G02680
## P11554_207 2.50928529 1.01617268 0.05198693 0.29214044 -0.28017788
## P11554_208 1.39850023 0.01265348 0.66191644 0.42064404 2.39270590
## P11554_209 1.26569457 -0.90486223 1.22152543 0.44202327 -0.56568425
## P11554_210 -0.02577165 0.35286424 1.05473582 0.37481972 0.12152621
## P11554_211 -0.49670016 -0.23416569 -0.08753393 -0.45033855 0.15866195
## P11554_212 0.19673336 -1.15241560 0.25336875 -0.36294041 1.55634665
## P11554_213 -1.22003841 1.46229257 -0.82549498 0.09372032 0.38247647
## P11554_214 -0.71371252 1.52937480 1.54521641 1.70436760 1.36025311
## P11554_215 -0.64027016 -0.22429098 0.61970382 1.55650292 0.42988827
## P11554_216 0.56102680 0.03520998 0.01482800 -0.47295597 -1.35906994
## P11554_217 0.44251010 -0.22224424 -0.59102142 0.14964522 -0.33903137
## P11554_218 -1.27838650 0.17753089 -2.37132935 -0.87611812 -0.39877862
## P11554_225 0.03830225 1.22026475 -1.12276113 -2.40973424 -0.57233015
## P11554_226 -0.02373941 -0.86618536 -0.34146161 -0.36814618 0.05430749
## P11554_227 -1.11101377 -1.56972940 1.34066794 -1.10940449 -1.14029395
## P11554_228 0.35994006 1.46067770 0.09812408 0.59936324 -0.82864952
## P11554_229 -0.89973492 -1.08970044 -0.99961527 -0.81605642 -1.29906503
## P11554_230 -0.36262517 -1.00344715 -0.52285592 1.23246762 0.32691468
## AT3G23890 AT3G48210 AT3G10270 AT1G69630 AT2G42720
## P11554_207 0.4747263 1.30189975 0.55884982 0.94097871 1.15274500
## P11554_208 1.2923942 1.30438718 1.08468650 0.45053961 1.12352388
## P11554_209 0.9777198 1.12887609 1.62749954 0.92260053 0.67990822
## P11554_210 0.4539379 0.33979780 -1.22894318 1.50916671 -0.04238059
## P11554_211 0.1975577 0.37155971 -0.18492336 0.20228865 -1.55926718
## P11554_212 0.4311020 0.42079045 -0.12129483 -1.04006536 -1.18067164
## P11554_213 0.6447525 -0.07135348 0.71105235 0.94075607 0.94179016
## P11554_214 1.1789711 0.29037019 0.02182673 -0.26578949 1.78311563
## P11554_215 0.6397487 1.34515165 1.77685262 1.98300407 1.64433051
## P11554_216 0.6002678 -0.05617984 0.34116044 -1.65419735 -0.41073085
## P11554_217 0.6567489 0.41949725 0.53380971 -0.17589654 -0.20972536
## P11554_218 0.3635734 -0.01418174 0.37842203 0.05545678 -1.23054980
## P11554_225 -1.4533920 -2.16352833 -0.76788776 -0.59589431 -0.31727510
## P11554_226 -1.4584113 -0.77206931 -0.67569562 -0.75586967 -0.04918682
## P11554_227 -1.0705713 -1.54726235 -1.19163950 -0.35369930 -0.80778999
## P11554_228 -1.2887196 -0.66009859 -1.97064664 0.22270384 -0.26614453
## P11554_229 -1.4728318 -0.38705532 -0.03012431 -1.02878503 -0.70479387
## P11554_230 -1.1675742 -1.25060113 -0.86300453 -1.35729792 -0.54689768
## AT1G50270 AT3G58210 AT4G17380 AT3G01410 AT3G61340
## P11554_207 1.8486276 -0.12253114 0.32580518 0.89537650 1.25149071
## P11554_208 1.0244050 1.03978493 1.33493705 0.73350723 0.86560227
## P11554_209 0.1162557 0.64868924 0.98355817 0.54101711 1.13222556
## P11554_210 0.6201343 -0.74994763 0.16701465 -0.27804284 -0.64029527
## P11554_211 -0.5713815 -1.00638078 -0.85867033 -0.44141105 -0.21916169
## P11554_212 -0.3236314 -0.22091364 0.29328110 -0.87512306 -0.80859676
## P11554_213 0.1984109 1.89863228 1.44880725 1.66530601 1.66661888
## P11554_214 1.9306451 1.89200147 1.34965526 1.73806214 1.31538863
## P11554_215 0.9750136 0.87743695 1.35471814 1.76062799 1.14837100
## P11554_216 -0.6299528 -1.02416284 -1.01282974 -0.52267308 0.01147291
## P11554_217 -0.9216412 0.42886318 -0.36400533 -0.65867593 0.11036858
## P11554_218 -1.3743764 -0.94783538 0.02623413 0.01597894 0.02712737
## P11554_225 0.4094586 -0.35393820 -0.14992908 -1.05782733 -0.41843931
## P11554_226 -0.4697676 -0.58406053 -0.12586442 -0.19526072 -0.68099504
## P11554_227 -1.7151617 -1.23056062 -0.52926344 -0.39038789 -1.12253970
## P11554_228 -0.2787312 -1.16433597 -1.58662763 -1.52572007 -0.91447041
## P11554_229 -0.6337507 0.65985576 -1.40941472 -0.47396013 -1.41364846
## P11554_230 -0.2045564 -0.04059709 -1.24740623 -0.93079382 -1.31051927
## AT5G65180 AT5G18810 AT1G67690 AT5G04130 AT1G79890 AT3G20475
## P11554_207 1.0901691 1.4908843 0.8371584 1.0702445 1.2056138 1.3679832
## P11554_208 1.2351624 1.1061465 1.3813777 1.2493431 1.0268523 1.0780559
## P11554_209 0.7689245 0.9977039 1.3499552 1.1168326 1.4416254 1.1629068
## P11554_210 -0.4538456 -0.5545175 -0.4357500 -0.5271782 -0.3988507 -0.8046798
## P11554_211 -0.6647288 -0.4608549 -1.1143086 -0.2318507 -0.7065301 -0.6463421
## P11554_212 -0.3454711 -0.4025878 -0.4501572 -0.1325102 -0.3357253 -0.3828723
## P11554_213 2.0025262 1.8829576 1.1970683 1.4242057 1.4038974 1.8402779
## P11554_214 1.6856641 0.8025901 1.7362130 1.4414487 1.6161444 1.1953351
## P11554_215 0.9974153 1.4770543 1.3790813 1.4368750 1.2699177 1.2563516
## P11554_216 -1.1469946 -0.3588351 -0.3820097 -0.1169846 -0.4224643 -0.5931881
## P11554_217 -0.4237974 -0.5001784 -0.3641219 -0.4244547 -0.7139891 -0.5122333
## P11554_218 -0.4825678 -0.4546359 -0.6262387 -0.2268235 -0.6843908 -0.2708118
## P11554_225 -0.7092009 -0.7806279 -0.9596258 -1.1856024 -0.2710567 -0.6308978
## P11554_226 -0.6292903 -0.8340000 -0.2564725 -0.9242380 -0.7154143 -0.2945882
## P11554_227 -0.4820260 -1.0238544 -0.4420835 -0.7918354 -0.6199425 -0.5600096
## P11554_228 -0.5513323 -0.7057090 -1.0753125 -1.1974295 -1.2978335 -1.2766234
## P11554_229 -1.2007440 -1.4127435 -0.8638316 -0.9983122 -0.7977086 -1.0921583
## P11554_230 -0.6898628 -0.2687922 -0.9109419 -0.9817301 -1.0001450 -0.8365060
## AT5G07660 AT5G48600 AT5G63920 AT3G10690 AT5G04110 AT5G57880
## P11554_207 1.2489549 1.1850839 1.1110978 1.1172395 1.1324380 1.542746472
## P11554_208 1.5530785 1.4112412 1.3349649 1.2201710 1.2236215 0.339784338
## P11554_209 1.0678267 1.2979243 1.4055262 1.2485323 1.1084209 1.439313449
## P11554_210 -0.5562306 -0.4601231 -0.5359858 -0.5977639 -0.4675613 0.267472917
## P11554_211 -0.5788684 -0.5431664 -0.5269688 -0.6266575 -0.4030146 -0.125525992
## P11554_212 -0.3248160 -0.3626244 -0.3857805 -0.4796994 -0.5424438 -0.006885189
## P11554_213 1.5205099 1.3788438 1.3414047 1.4091492 1.6178900 1.061308161
## P11554_214 1.1882190 1.3865620 1.5132862 1.4355288 1.4823474 1.438043312
## P11554_215 1.5131207 1.4561109 1.3596463 1.6310324 1.4997431 1.007007997
## P11554_216 -0.7627030 -0.6694035 -0.5300699 -0.4004922 -0.5299081 -0.501863766
## P11554_217 -0.8524258 -0.5402411 -0.5065896 -0.4627756 -0.6370566 -1.353167199
## P11554_218 -0.6409672 -0.5947747 -0.4046068 -0.4285505 -0.5397953 -0.519782469
## P11554_225 -0.8694127 -0.8902324 -0.7656418 -0.7269294 -0.6318833 -1.937149859
## P11554_226 -0.4358695 -0.6540643 -0.6934622 -0.5981473 -0.6965451 -0.031514074
## P11554_227 -0.7069094 -0.5556733 -0.6733024 -0.7213687 -0.6486021 -1.066138767
## P11554_228 -1.0280267 -1.0114518 -1.1549999 -1.0530173 -0.9509846 -0.715476766
## P11554_229 -0.7422745 -0.9858013 -1.0363476 -0.9104149 -1.1334433 -0.295329754
## P11554_230 -0.5932058 -0.8482098 -0.8521707 -1.0558367 -0.8832228 -0.542842812
## AT1G72270 AT4G35520 AT2G27170 AT5G15920
## P11554_207 1.5074254 1.03731889 1.1614486 0.980447541
## P11554_208 1.3130577 1.51895097 1.4230079 1.493339090
## P11554_209 1.3511359 1.92672732 1.2904145 0.690155686
## P11554_210 -0.4096606 -0.29266537 -0.5521039 -0.412868695
## P11554_211 -0.4095291 0.08706676 -0.1502148 -0.316369855
## P11554_212 -0.1375077 -0.03653568 -0.1566788 0.002796631
## P11554_213 0.4855110 1.38158346 0.8561628 1.186285126
## P11554_214 1.8159623 0.97771678 1.3861563 1.580953974
## P11554_215 0.9837054 0.80479466 1.5715921 1.399090575
## P11554_216 0.1021732 -0.95233375 -0.5870010 -0.393701180
## P11554_217 -0.5097416 -0.82224508 -0.4865800 -0.168197399
## P11554_218 -0.5183853 -0.66738276 -0.3690833 -0.049899161
## P11554_225 -0.9609499 -1.09431314 -1.4835051 -1.602892032
## P11554_226 -0.8155169 -0.98583571 -1.2378370 -1.010320364
## P11554_227 -0.6354613 -0.70383867 -0.9138657 -1.061562706
## P11554_228 -1.0967536 -0.67371441 -0.5955745 -0.471088286
## P11554_229 -0.5556710 -0.84607737 -0.8745139 -1.352528930
## P11554_230 -1.5097940 -0.65921689 -0.2818241 -0.493640016
##
## $`GO:0007059`$rowDendrogram
## 'dendrogram' with 2 branches and 42 members total, at height 2.232392
##
## $`GO:0007059`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0007059`$breaks
## [1] -2.53655125 -2.48582022 -2.43508920 -2.38435817 -2.33362715 -2.28289612
## [7] -2.23216510 -2.18143407 -2.13070305 -2.07997202 -2.02924100 -1.97850997
## [13] -1.92777895 -1.87704792 -1.82631690 -1.77558587 -1.72485485 -1.67412382
## [19] -1.62339280 -1.57266177 -1.52193075 -1.47119972 -1.42046870 -1.36973767
## [25] -1.31900665 -1.26827562 -1.21754460 -1.16681357 -1.11608255 -1.06535152
## [31] -1.01462050 -0.96388947 -0.91315845 -0.86242742 -0.81169640 -0.76096537
## [37] -0.71023435 -0.65950332 -0.60877230 -0.55804127 -0.50731025 -0.45657922
## [43] -0.40584820 -0.35511717 -0.30438615 -0.25365512 -0.20292410 -0.15219307
## [49] -0.10146205 -0.05073102 0.00000000 0.05073102 0.10146205 0.15219307
## [55] 0.20292410 0.25365512 0.30438615 0.35511717 0.40584820 0.45657922
## [61] 0.50731025 0.55804127 0.60877230 0.65950332 0.71023435 0.76096537
## [67] 0.81169640 0.86242742 0.91315845 0.96388947 1.01462050 1.06535152
## [73] 1.11608255 1.16681357 1.21754460 1.26827562 1.31900665 1.36973767
## [79] 1.42046870 1.47119972 1.52193075 1.57266177 1.62339280 1.67412382
## [85] 1.72485485 1.77558587 1.82631690 1.87704792 1.92777895 1.97850997
## [91] 2.02924100 2.07997202 2.13070305 2.18143407 2.23216510 2.28289612
## [97] 2.33362715 2.38435817 2.43508920 2.48582022 2.53655125
##
## $`GO:0007059`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0007059`$colorTable
## low high color
## 1 -2.53655125 -2.48582022 #0000FF
## 2 -2.48582022 -2.43508920 #0505FF
## 3 -2.43508920 -2.38435817 #0A0AFF
## 4 -2.38435817 -2.33362715 #0F0FFF
## 5 -2.33362715 -2.28289612 #1414FF
## 6 -2.28289612 -2.23216510 #1919FF
## 7 -2.23216510 -2.18143407 #1E1EFF
## 8 -2.18143407 -2.13070305 #2424FF
## 9 -2.13070305 -2.07997202 #2929FF
## 10 -2.07997202 -2.02924100 #2E2EFF
## 11 -2.02924100 -1.97850997 #3333FF
## 12 -1.97850997 -1.92777895 #3838FF
## 13 -1.92777895 -1.87704792 #3D3DFF
## 14 -1.87704792 -1.82631690 #4242FF
## 15 -1.82631690 -1.77558587 #4848FF
## 16 -1.77558587 -1.72485485 #4D4DFF
## 17 -1.72485485 -1.67412382 #5252FF
## 18 -1.67412382 -1.62339280 #5757FF
## 19 -1.62339280 -1.57266177 #5C5CFF
## 20 -1.57266177 -1.52193075 #6161FF
## 21 -1.52193075 -1.47119972 #6767FF
## 22 -1.47119972 -1.42046870 #6C6CFF
## 23 -1.42046870 -1.36973767 #7171FF
## 24 -1.36973767 -1.31900665 #7676FF
## 25 -1.31900665 -1.26827562 #7B7BFF
## 26 -1.26827562 -1.21754460 #8080FF
## 27 -1.21754460 -1.16681357 #8585FF
## 28 -1.16681357 -1.11608255 #8B8BFF
## 29 -1.11608255 -1.06535152 #9090FF
## 30 -1.06535152 -1.01462050 #9595FF
## 31 -1.01462050 -0.96388947 #9A9AFF
## 32 -0.96388947 -0.91315845 #9F9FFF
## 33 -0.91315845 -0.86242742 #A4A4FF
## 34 -0.86242742 -0.81169640 #AAAAFF
## 35 -0.81169640 -0.76096537 #AFAFFF
## 36 -0.76096537 -0.71023435 #B4B4FF
## 37 -0.71023435 -0.65950332 #B9B9FF
## 38 -0.65950332 -0.60877230 #BEBEFF
## 39 -0.60877230 -0.55804127 #C3C3FF
## 40 -0.55804127 -0.50731025 #C8C8FF
## 41 -0.50731025 -0.45657922 #CECEFF
## 42 -0.45657922 -0.40584820 #D3D3FF
## 43 -0.40584820 -0.35511717 #D8D8FF
## 44 -0.35511717 -0.30438615 #DDDDFF
## 45 -0.30438615 -0.25365512 #E2E2FF
## 46 -0.25365512 -0.20292410 #E7E7FF
## 47 -0.20292410 -0.15219307 #ECECFF
## 48 -0.15219307 -0.10146205 #F2F2FF
## 49 -0.10146205 -0.05073102 #F7F7FF
## 50 -0.05073102 0.00000000 #FCFCFF
## 51 0.00000000 0.05073102 #FFFCFC
## 52 0.05073102 0.10146205 #FFF7F7
## 53 0.10146205 0.15219307 #FFF2F2
## 54 0.15219307 0.20292410 #FFECEC
## 55 0.20292410 0.25365512 #FFE7E7
## 56 0.25365512 0.30438615 #FFE2E2
## 57 0.30438615 0.35511717 #FFDDDD
## 58 0.35511717 0.40584820 #FFD8D8
## 59 0.40584820 0.45657922 #FFD3D3
## 60 0.45657922 0.50731025 #FFCECE
## 61 0.50731025 0.55804127 #FFC8C8
## 62 0.55804127 0.60877230 #FFC3C3
## 63 0.60877230 0.65950332 #FFBEBE
## 64 0.65950332 0.71023435 #FFB9B9
## 65 0.71023435 0.76096537 #FFB4B4
## 66 0.76096537 0.81169640 #FFAFAF
## 67 0.81169640 0.86242742 #FFA9A9
## 68 0.86242742 0.91315845 #FFA4A4
## 69 0.91315845 0.96388947 #FF9F9F
## 70 0.96388947 1.01462050 #FF9A9A
## 71 1.01462050 1.06535152 #FF9595
## 72 1.06535152 1.11608255 #FF9090
## 73 1.11608255 1.16681357 #FF8B8B
## 74 1.16681357 1.21754460 #FF8585
## 75 1.21754460 1.26827562 #FF8080
## 76 1.26827562 1.31900665 #FF7B7B
## 77 1.31900665 1.36973767 #FF7676
## 78 1.36973767 1.42046870 #FF7171
## 79 1.42046870 1.47119972 #FF6C6C
## 80 1.47119972 1.52193075 #FF6767
## 81 1.52193075 1.57266177 #FF6161
## 82 1.57266177 1.62339280 #FF5C5C
## 83 1.62339280 1.67412382 #FF5757
## 84 1.67412382 1.72485485 #FF5252
## 85 1.72485485 1.77558587 #FF4D4D
## 86 1.77558587 1.82631690 #FF4848
## 87 1.82631690 1.87704792 #FF4242
## 88 1.87704792 1.92777895 #FF3D3D
## 89 1.92777895 1.97850997 #FF3838
## 90 1.97850997 2.02924100 #FF3333
## 91 2.02924100 2.07997202 #FF2E2E
## 92 2.07997202 2.13070305 #FF2929
## 93 2.13070305 2.18143407 #FF2424
## 94 2.18143407 2.23216510 #FF1E1E
## 95 2.23216510 2.28289612 #FF1919
## 96 2.28289612 2.33362715 #FF1414
## 97 2.33362715 2.38435817 #FF0F0F
## 98 2.38435817 2.43508920 #FF0A0A
## 99 2.43508920 2.48582022 #FF0505
## 100 2.48582022 2.53655125 #FF0000
##
## $`GO:0007059`$layout
## $`GO:0007059`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0007059`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0007059`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0051301`
## $`GO:0051301`$rowInd
## [1] 3 10 57 26 6 56 50 64 45 16 54 69 18 41 27 21 22 55 71 17 29 47 53 65 74
## [26] 60 70 12 23 34 5 1 48 43 63 68 67 52 39 44 59 51 42 46 24 13 38 2 11 58
## [51] 15 9 61 36 62 32 35 8 20 14 28 25 31 37 19 40 72 73 66 7 30 33 4 49
##
## $`GO:0051301`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0051301`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0051301`$carpet
## AT1G13980 AT1G56350 AT4G30080 AT2G44190 AT1G48410
## P11554_207 -2.02583091 0.05597583 -0.02004782 0.02359938 -1.52185850
## P11554_208 -0.20041671 -0.43149410 -0.26278260 0.09597322 0.05451137
## P11554_209 -0.77853339 0.89216461 -0.14882417 -0.11751802 0.29427536
## P11554_210 1.37517789 0.14658224 0.83865422 0.66339577 -1.20210992
## P11554_211 0.60232073 1.46649752 0.60461351 1.35345693 -1.01390535
## P11554_212 1.00262403 0.40344901 0.68022917 0.52050707 -0.17301048
## P11554_213 -0.11012221 2.18600030 0.17257126 -0.04625256 0.48140777
## P11554_214 0.27832275 0.36738448 0.75705191 -0.28248273 0.93994463
## P11554_215 -0.65343346 0.35603822 -0.02358148 -0.13526557 0.46290840
## P11554_216 0.73486940 1.15975672 1.62721135 1.62573798 0.73776929
## P11554_217 0.83286493 -0.67708219 1.39469401 1.46636470 1.72800670
## P11554_218 -0.07013975 -0.15642626 1.12173902 0.57292648 1.12843318
## P11554_225 1.89485945 -0.47482011 -1.44695738 -0.76362532 -1.93815311
## P11554_226 -1.12244910 -1.15597632 -1.62982454 -2.05398874 -0.82091856
## P11554_227 0.09660717 -0.89260776 -1.63662941 -1.85712639 0.47505566
## P11554_228 0.07147299 -1.79814904 -0.40203256 0.20954856 -0.70839668
## P11554_229 -0.45833267 -1.01726171 -0.74319097 -0.86552132 0.20531390
## P11554_230 -1.46986114 -0.43003145 -0.88289354 -0.40972946 0.87072635
## AT4G26740 AT4G03240 AT5G15540 AT4G00150 AT1G78580 AT4G21800
## P11554_207 -0.5052412 -0.7780148 0.50622693 0.54985365 -0.1750517 0.75300430
## P11554_208 -0.5052412 0.4453293 1.60179206 0.24737007 1.1377001 1.22746442
## P11554_209 -0.5052412 0.1171017 0.89996375 0.01148859 0.9926790 1.39238146
## P11554_210 -0.5052412 -0.9914645 0.02002549 0.23778851 1.4102571 0.96792346
## P11554_211 -0.5052412 -0.1958370 -0.47800680 -0.06570887 1.3100664 -0.21283066
## P11554_212 -0.5052412 0.9297783 1.07368450 2.57765367 1.3142760 0.46157872
## P11554_213 -0.5052412 0.2478037 -0.09223314 1.22091714 -0.5517982 0.30849479
## P11554_214 2.4562049 1.1554786 0.04969077 -0.83822176 0.9309133 0.57418187
## P11554_215 -0.5052412 0.8084441 0.66905538 -1.08914640 -0.3919688 1.29496809
## P11554_216 1.9647210 0.2602740 -1.85836392 0.50900187 -0.4560700 -0.91028829
## P11554_217 -0.5052412 -2.7365670 -2.10724346 -1.08727008 -0.3980925 -0.99511114
## P11554_218 -0.5052412 -1.1356889 -1.43258638 -0.97489268 0.7549452 -0.47512285
## P11554_225 -0.5052412 0.4073613 0.63580391 -0.34691682 -0.8474471 -1.84499542
## P11554_226 -0.5052412 -0.5052130 -0.10201199 0.54432011 -0.8051162 -1.00990221
## P11554_227 1.2384123 -0.3514988 -0.50690603 -1.32882176 -1.8048390 -1.73897148
## P11554_228 -0.5052412 0.2119025 0.24771539 0.48799436 -1.1307170 -0.22619247
## P11554_229 -0.5052412 0.5155110 -0.04656693 -1.20083311 -0.2829498 0.37939276
## P11554_230 1.4140379 1.5952997 0.91996045 0.54542352 -1.0067866 0.05402464
## AT5G27540 AT2G20000 AT3G59420 AT2G44950 AT2G34710
## P11554_207 -0.003296869 -0.25898756 0.42694502 0.4900622 1.26674556
## P11554_208 -0.002503470 -0.23855749 0.18773868 1.1115269 0.90672661
## P11554_209 1.689562293 0.61776725 0.86407768 1.0886149 1.43933069
## P11554_210 -0.985319881 -0.37899176 0.26081816 -0.4606751 -0.08884232
## P11554_211 -1.468707789 -1.31015858 -0.10258101 0.3570595 -0.61131914
## P11554_212 -0.149352211 -0.88722495 0.09698469 1.2492092 -0.02289997
## P11554_213 1.865794290 1.48362485 1.75151915 0.9285465 1.01836971
## P11554_214 0.976521702 0.97046793 -0.46488134 0.3151900 1.73925127
## P11554_215 1.495195162 1.61365014 0.93136951 1.6156572 0.85363252
## P11554_216 -1.208254913 -1.61797650 -1.79415625 -1.0052641 0.30859762
## P11554_217 -1.092607158 -0.07872542 0.07070032 -0.7933688 -0.70656298
## P11554_218 -0.064722875 -0.46877238 0.73245553 -1.3730689 -0.82758621
## P11554_225 -0.375129925 0.43620663 -0.11666044 -0.4757028 -0.46916182
## P11554_226 0.361240460 1.09939566 -0.41463830 -0.5190658 -0.88198622
## P11554_227 0.440412765 0.97868799 -1.79415625 -0.2919003 -0.63047876
## P11554_228 -0.955794081 -0.90810742 -0.02949492 -1.5057745 -1.54602210
## P11554_229 -0.536600828 -1.39831549 -1.79415625 -1.4205892 -0.26719085
## P11554_230 0.013563327 0.34601710 1.18811601 0.6895433 -1.48060359
## AT2G34780 AT4G22970 AT5G40770 AT1G80620 AT2G47420 AT4G01560
## P11554_207 0.9040177 1.0147745 0.9927272 1.0182398 1.0669535 1.0476259
## P11554_208 1.1254688 1.0247614 1.2503838 1.3144156 1.2993738 1.1122329
## P11554_209 1.1427176 1.0334445 1.1668868 1.1141369 1.0293368 1.2261864
## P11554_210 -0.3438493 -0.4749653 -0.4859794 -0.7624893 -0.6780071 -0.6973430
## P11554_211 -0.3378913 -0.6539722 -0.5692513 -0.4683782 -0.3963653 -0.6785019
## P11554_212 -0.3331456 -0.0966451 -0.4953855 -0.5599108 -0.7769252 -0.4968660
## P11554_213 1.5416957 1.5440869 1.4794205 1.3903009 1.4552934 1.5076958
## P11554_214 1.3400337 1.5993432 1.3871415 1.4361724 1.6483672 1.4035466
## P11554_215 1.6765209 1.6275016 1.5440418 1.6058363 1.3765885 1.7132453
## P11554_216 -0.4370116 -0.7503155 -0.2935312 -0.3827245 -0.3763019 -0.4694867
## P11554_217 -0.1521109 -0.4018938 -0.2533602 -0.2363987 -0.4332461 -0.5923283
## P11554_218 -0.4942792 -0.4635115 -0.2375526 -0.2294486 -0.4691402 -0.4595016
## P11554_225 -0.4054307 -0.3896783 -0.5804708 -0.3814603 -0.5245094 -0.5032799
## P11554_226 -0.9593661 -0.6829076 -0.5961183 -0.7129492 -0.3471433 -0.4996717
## P11554_227 -0.8593822 -0.6794022 -0.6958409 -0.7772118 -0.4302694 -0.4836665
## P11554_228 -1.1262522 -0.8900384 -1.3551797 -1.2098105 -0.9683017 -1.0880630
## P11554_229 -1.3961275 -1.1564622 -1.0342415 -1.0802694 -1.1133669 -1.0551579
## P11554_230 -0.8856078 -1.2041202 -1.2236903 -1.0780506 -1.3623365 -0.9866664
## AT4G21100 AT5G16750 AT5G62440 AT4G32720 AT5G38110 AT1G59760
## P11554_207 1.1009617 1.0002691 1.1855783 1.1434216 1.2332156 0.8927473
## P11554_208 1.0616974 1.1233640 1.2231847 1.3277204 1.0933375 0.9607755
## P11554_209 1.1892801 1.0899307 1.2195419 1.1467105 1.4594556 0.9144042
## P11554_210 -0.6806545 -0.4804685 -0.6328770 -0.6074427 -0.6858124 -0.9672855
## P11554_211 -0.5930692 -0.6461171 -0.6039677 -0.5737664 -0.5603448 -0.6710644
## P11554_212 -0.6355299 -0.5433900 -0.6606093 -0.4859506 -0.7769773 -0.4176623
## P11554_213 1.4079178 1.5211086 1.4452430 1.4352732 1.1060374 1.5798527
## P11554_214 1.4482780 1.5641705 1.4081227 1.4452409 1.4858847 1.7063451
## P11554_215 1.7898439 1.6917209 1.6217933 1.6441208 1.6400713 1.7389765
## P11554_216 -0.5885128 -0.5124627 -0.3606747 -0.5423087 -0.6314178 -0.7030201
## P11554_217 -0.7343403 -0.4682845 -0.4772281 -0.5995787 -0.2407016 -0.3876487
## P11554_218 -0.3896834 -0.4422557 -0.5054026 -0.5448706 -0.4664166 -0.3517075
## P11554_225 -0.4253893 -0.4792011 -0.7094360 -0.6585981 -0.7467310 -0.6522212
## P11554_226 -0.6113604 -0.6428803 -0.6825387 -0.7212674 -0.5180344 -0.5694999
## P11554_227 -0.3267121 -0.7040329 -0.5987865 -0.7626961 -0.4715177 -0.4421913
## P11554_228 -1.1151522 -1.0676933 -1.0310631 -0.9579297 -0.9738838 -1.0458788
## P11554_229 -0.9734629 -1.1019759 -0.8533728 -0.8440643 -1.1731618 -1.2331797
## P11554_230 -0.9241119 -0.9018018 -0.9875074 -0.8440141 -0.7730027 -0.3517421
## AT2G38280 AT3G18730 AT1G47870 AT1G01370 AT4G02460 AT3G60830
## P11554_207 1.0172914 1.1104582 1.1979456 1.0774924 1.1040710 1.0154352
## P11554_208 1.2126982 1.3946866 1.3673092 0.9760469 1.1458063 0.9826750
## P11554_209 1.3231821 1.5015212 1.5439056 1.3844050 1.5061699 1.3673070
## P11554_210 -0.6538808 -0.5431913 -0.4304366 -0.2086459 -0.2466275 -0.6658254
## P11554_211 -0.5841784 -0.5149633 -0.6393645 -0.5515003 -0.3151451 -0.8824222
## P11554_212 -0.4789596 -0.2945135 -0.2838209 -0.5661568 -0.2866156 -0.8705249
## P11554_213 1.4613942 1.2776922 1.3609523 1.6468283 1.3806348 1.9621926
## P11554_214 1.4485565 1.3089160 1.2891883 1.1982197 1.3223978 1.0680331
## P11554_215 1.4043052 1.4848328 1.2938822 1.6721586 1.4811517 1.4278835
## P11554_216 -0.8842228 -0.6740330 -0.8668406 -0.5492081 -0.6866920 -0.6499329
## P11554_217 -0.8497017 -0.6116845 -0.6008572 -0.4413494 -0.4625901 -0.5935191
## P11554_218 -0.7758341 -0.6914168 -0.5938030 -0.5609742 -0.5323456 0.1134767
## P11554_225 -0.1657288 -0.5769586 -0.4490311 -0.8324846 -0.9644814 -0.6850750
## P11554_226 -0.1603307 -0.6702442 -0.5134674 -0.9305390 -0.9143301 -0.5374909
## P11554_227 -0.1675804 -0.5087445 -0.6359517 -0.5722250 -0.5973125 -0.5715524
## P11554_228 -1.1401093 -1.0424832 -0.9660095 -1.1861148 -1.2898066 -1.1769980
## P11554_229 -1.1425365 -1.1061925 -1.1612209 -0.6316731 -0.7971661 -0.7429850
## P11554_230 -0.8643645 -0.8436819 -0.9123799 -0.9242798 -0.8471189 -0.5606772
## AT5G13480 AT5G22370 AT5G22130 AT4G15900 AT3G49600
## P11554_207 0.53589180 0.94309924 1.11933107 0.6149923 1.2283031
## P11554_208 0.79146688 0.88799945 1.02068301 1.2306433 1.6137918
## P11554_209 2.06947285 0.97490658 1.25305568 1.3607076 1.5729629
## P11554_210 -0.46248481 -0.26690351 -0.49202963 -0.5563394 -0.9633772
## P11554_211 -0.09030563 -0.44953720 -0.39932985 -0.5448430 -0.3083672
## P11554_212 -0.29697587 -0.28620717 -0.27268512 -0.3716877 -0.3906767
## P11554_213 1.47634527 1.45325835 1.51027069 1.2964098 1.2689877
## P11554_214 0.82349210 1.29752874 1.48281483 1.4323680 1.1408983
## P11554_215 1.22130222 1.60540180 1.22695839 1.4978277 0.8601132
## P11554_216 -0.51355355 -0.15236766 -0.41827897 -0.4518310 -1.0007204
## P11554_217 -0.20151187 0.16612519 -0.55911420 -0.4235795 -0.5860091
## P11554_218 -0.09885862 -0.08574135 -0.67307494 -0.2542934 -0.7900491
## P11554_225 -0.85361755 -0.52549308 -0.46693343 -0.5953220 -0.5666813
## P11554_226 -0.04064397 -0.56773673 -0.08860887 0.0455064 0.4215722
## P11554_227 -0.36262705 -0.60511867 -0.20033974 -0.1928980 -0.7522507
## P11554_228 -1.98622668 -1.65515498 -1.27273720 -1.6385976 -0.9907735
## P11554_229 -1.02437484 -1.63499193 -1.46011447 -1.2935612 -0.9905778
## P11554_230 -0.98679067 -1.09906706 -1.30986724 -1.1555024 -0.7671463
## AT3G61140 AT4G32010 AT4G11140 AT3G60630 AT4G00310 AT2G38560
## P11554_207 0.86932974 0.5590480 0.8790719 1.3849262 1.09065942 1.5026279
## P11554_208 1.19502555 1.4523791 -0.5763852 0.7883268 0.92267389 1.1192749
## P11554_209 1.42514622 1.5577850 -0.5763852 0.4605700 0.29559469 0.2572377
## P11554_210 -1.03828715 -1.1701386 -0.5763852 -0.4061729 -0.55795013 -0.6167697
## P11554_211 -0.84195229 -0.6786439 -0.5763852 -0.4032363 -1.19586459 -0.9442658
## P11554_212 -0.72392117 -0.6277934 -0.5763852 -0.7037834 -0.56710283 -0.7135531
## P11554_213 1.42368342 1.3126475 2.2689178 1.3349224 1.83866279 1.8433457
## P11554_214 1.27561224 1.4621463 1.5562792 1.5488488 1.06269802 1.6504905
## P11554_215 1.51643168 1.2466520 1.8686306 0.9653812 1.76194068 1.2738432
## P11554_216 -0.90887905 -0.9411770 -0.5763852 0.3235036 -0.13301420 -0.4735182
## P11554_217 -0.32633345 -0.8318101 0.9201088 0.3579746 -0.39945081 -0.6570428
## P11554_218 -0.69405124 -0.6409034 -0.5763852 -0.5225392 0.01059674 -0.3260785
## P11554_225 -0.06463421 -0.1910948 -0.5763852 0.7429130 0.52186609 -0.0461024
## P11554_226 0.10425120 -0.2892703 -0.5763852 -1.0240739 -0.67212091 -0.6887886
## P11554_227 -0.26340724 0.1982398 -0.5763852 -1.1978093 -1.46476875 -0.8356106
## P11554_228 -1.16988796 -1.1821572 -0.5763852 -0.7548691 -0.78209707 -0.6048684
## P11554_229 -0.69889119 -0.2992072 -0.5763852 -1.3720894 -0.99874758 -1.0702835
## P11554_230 -1.07923510 -0.9367019 -0.5763852 -1.5227930 -0.73357545 -0.6699381
## AT1G66740 AT3G49240 AT1G10270 AT1G57820 AT4G31160
## P11554_207 1.2608632 1.189994e+00 0.941882536 0.3595012 0.5300181
## P11554_208 1.3817413 1.047152e+00 1.277041760 0.9980755 1.2717835
## P11554_209 0.3009029 8.334214e-01 0.846721551 1.3659949 1.0656650
## P11554_210 -0.9326347 -4.128209e-01 -0.002343113 -0.7097144 -0.8738082
## P11554_211 -0.7907723 -2.417889e-01 0.082127117 -0.7075302 -0.2494166
## P11554_212 -0.4160252 -2.527077e-01 0.187705681 -0.4287885 -0.2713102
## P11554_213 1.4745948 1.609544e+00 1.182477528 1.3732173 1.7603126
## P11554_214 1.5376138 1.400800e+00 1.477589338 1.5306195 1.8437133
## P11554_215 1.5624647 1.443258e+00 1.176205593 1.2481212 1.1984330
## P11554_216 -0.9159843 3.185032e-05 -0.117196103 -0.2094874 -0.5308218
## P11554_217 -0.7147934 -1.893314e-02 0.121545791 0.2428382 -0.2358867
## P11554_218 -0.7883952 -2.147730e-01 0.037528982 0.4524641 -0.5649845
## P11554_225 0.1001368 -1.140138e+00 -1.062484309 -1.7248064 -0.8457845
## P11554_226 -0.9500095 -1.112568e+00 -1.248272484 -0.9743803 -1.1179412
## P11554_227 -0.3482732 -1.093439e+00 -1.093486798 -1.3859117 -1.1145662
## P11554_228 -0.2495576 -9.715734e-01 -1.318684819 -0.8391944 -0.7134727
## P11554_229 -0.2306910 -1.093349e+00 -1.316764446 -0.2596083 -0.7949240
## P11554_230 -1.2811810 -9.721111e-01 -1.171593807 -0.3314103 -0.3570088
## AT1G71830 AT1G55350 AT4G32880 AT3G24650 AT5G09810 AT3G10220
## P11554_207 0.21461865 0.3981399 -0.03883533 -0.3425598 -1.03737321 -1.1071672
## P11554_208 0.29668321 0.7696070 0.16069296 -0.3425598 -0.63618019 -0.4150851
## P11554_209 0.11507326 1.0460612 -0.06216564 -0.3425598 -0.15134967 -1.7127357
## P11554_210 0.06344933 -0.9759153 -0.29835789 -0.3425598 -1.44998203 -1.0175325
## P11554_211 0.08600105 -0.7706494 -0.54969984 -0.3425598 -1.48464756 -1.1452617
## P11554_212 -0.21202354 -0.5640309 -1.02409776 -0.3425598 -1.49138287 -0.4971921
## P11554_213 1.75866680 1.4071312 1.28854703 2.5146476 0.73715036 0.5103835
## P11554_214 1.25516385 1.4432899 0.47354274 -0.3425598 0.55036730 0.2896028
## P11554_215 1.76694588 1.2792771 0.24770215 -0.3425598 0.19409483 1.3587569
## P11554_216 0.63340361 0.4382059 -1.25987043 -0.3425598 0.40676596 -0.9218281
## P11554_217 0.39160787 0.8949184 -1.77872157 -0.3425598 0.58110490 -1.0586191
## P11554_218 0.39975571 0.5648357 -0.98526659 -0.3425598 0.89776719 0.3855977
## P11554_225 -0.92656710 -0.7338903 2.02358996 2.9663094 0.64590475 0.4654619
## P11554_226 -0.49881481 -0.9906513 1.19333973 -0.3425598 1.76030562 1.5142233
## P11554_227 -1.27897573 -0.7686354 1.32374553 -0.3425598 1.43463422 1.1810544
## P11554_228 -1.31417138 -0.9084687 -0.71944537 -0.3425598 -1.08996838 0.2837827
## P11554_229 -1.51294268 -1.5332359 -0.18724557 -0.3425598 0.04004043 0.9460597
## P11554_230 -1.23787396 -0.9959890 0.19254589 -0.3425598 0.09274835 0.9404988
## AT3G21510 AT1G55180 AT2G28350 AT1G69670 AT2G45160
## P11554_207 -1.33722137 -0.2357023 -1.03047732 -1.13844310 -0.7241674
## P11554_208 0.08451992 -0.2357023 -1.40731993 -0.76663111 -0.7624029
## P11554_209 0.22005695 -0.2357023 -1.47446048 -0.17376929 -0.5436184
## P11554_210 0.74729385 -0.2357023 -0.02819102 1.09229077 0.5720496
## P11554_211 0.76411028 -0.2357023 0.02762297 0.82201372 0.6151379
## P11554_212 0.01940049 -0.2357023 -0.73529811 0.79300194 0.3622695
## P11554_213 -1.33722137 -0.2357023 -0.35203606 -1.09264478 -1.4818147
## P11554_214 0.01116223 -0.2357023 -0.85795100 -1.46055381 -0.7894277
## P11554_215 0.04563998 -0.2357023 -0.28165257 -2.13927409 -1.1219562
## P11554_216 -1.33722137 -0.2357023 0.46245940 0.01181905 0.9302269
## P11554_217 -1.33722137 -0.2357023 -0.06854129 -0.24486940 -0.3465013
## P11554_218 -0.05535010 -0.2357023 -0.98409451 -0.08097323 -0.6303630
## P11554_225 -1.33722137 -0.2357023 1.88290471 0.61904418 0.5939082
## P11554_226 0.06212751 -0.2357023 1.47826030 0.54683380 -0.4042964
## P11554_227 1.41131419 -0.2357023 0.63033331 0.10637691 -0.9601606
## P11554_228 1.76192662 -0.2357023 1.46306425 1.72290413 1.9540213
## P11554_229 0.33089119 -0.2357023 0.76655264 0.69221312 1.7553891
## P11554_230 1.28301372 4.0069384 0.50882469 0.69066119 0.9817063
## AT2G43790 AT3G09840 AT3G27670 AT2G26890 AT3G51810
## P11554_207 -1.642028520 -1.26017568 -1.35978327 -1.7662982 -0.89936221
## P11554_208 -1.378239200 -0.94529898 -1.00959461 -0.8876377 -0.89936221
## P11554_209 -0.767815776 -0.71804161 -1.26017940 -0.6906474 -0.89936221
## P11554_210 -0.017636797 0.28892589 0.72644963 0.4075192 -0.89936221
## P11554_211 -0.011344501 0.24666024 0.85645467 0.6365053 0.37210560
## P11554_212 0.207746079 0.37005714 0.78897425 1.0158025 0.84137152
## P11554_213 -1.220594481 -1.46151894 -1.27818416 -1.6717685 -0.89936221
## P11554_214 -1.075147238 -1.29519877 -0.93241475 -0.9003710 -0.89936221
## P11554_215 -1.210697824 -1.61393530 -1.68881132 -1.5948855 -0.89936221
## P11554_216 0.211249286 0.01874048 0.12375581 0.6694764 -0.89936221
## P11554_217 0.432490405 0.21481830 0.15563697 0.6462947 -0.89936221
## P11554_218 0.008000941 0.31283516 0.06929903 0.1053888 0.05049825
## P11554_225 0.654679979 0.42313858 0.32173692 0.5415800 1.28374443
## P11554_226 1.227081442 0.52074281 0.13993830 0.7739583 0.89616913
## P11554_227 0.869037797 0.54832615 0.79759081 1.1816594 1.13728947
## P11554_228 0.949608743 1.19096278 1.16798405 -0.2234032 0.42704056
## P11554_229 1.287856721 1.57973631 0.80199293 0.6500261 1.24079898
## P11554_230 1.475752943 1.57922543 1.57915413 1.1068008 1.84524196
## AT5G46210 AT5G60410 AT5G20490 AT1G50030 AT3G08850 AT3G12400
## P11554_207 -1.43773457 -1.7224402 -1.7279927 -1.57146041 -1.3513721 -1.31674179
## P11554_208 -0.71147110 -1.3380981 -1.4455369 -1.03500289 -0.9888080 -1.15081918
## P11554_209 -0.81933305 -0.4263909 -1.2208266 -0.77757380 -1.3908492 -1.45510761
## P11554_210 0.17242829 0.3838773 0.5099163 0.37821970 0.8149700 1.10879402
## P11554_211 0.15090207 -0.2377363 0.5664035 0.61741333 0.8674527 1.27136720
## P11554_212 0.76376656 0.2671240 0.7821475 0.90970487 1.0245027 0.46921208
## P11554_213 -0.69326984 -1.0146178 -0.9684897 -1.58017706 -0.9819609 -0.96664716
## P11554_214 -1.41013147 -1.0815673 -0.8823615 -1.10470153 -1.2771934 -1.15079954
## P11554_215 -0.67010863 -0.3549440 -0.8927406 -1.26359068 -1.0811242 -1.24056602
## P11554_216 -0.18742470 -0.7733691 0.9468482 0.93681239 0.6947820 1.19407342
## P11554_217 -0.33467546 0.5214622 1.1570398 1.04446139 0.5498794 1.27300797
## P11554_218 -0.29586220 -0.3605248 1.0731112 0.61271433 0.2983558 0.75450925
## P11554_225 0.01660766 0.1017572 -0.3642273 -0.03548032 -0.2427112 -0.48437398
## P11554_226 0.42536309 0.4062798 -0.2843946 -0.45186476 -0.5601705 -0.09247390
## P11554_227 0.13533536 0.9106027 -0.2021416 0.07053477 -0.1215778 0.08978476
## P11554_228 0.55480342 1.5149320 1.0333877 1.11075512 1.0273757 0.46067841
## P11554_229 2.30850627 1.4812144 0.6633695 0.83237482 1.2618455 0.86062530
## P11554_230 2.03229831 1.7224388 1.2564880 1.30686074 1.4566035 0.37547678
## AT1G17580 AT4G02570
## P11554_207 -2.316724466 -1.83677238
## P11554_208 -0.519997736 -0.37036370
## P11554_209 -0.759644880 0.35794509
## P11554_210 0.173325847 0.31933947
## P11554_211 0.470355678 0.41802093
## P11554_212 0.980310992 1.23360801
## P11554_213 -1.199715425 -1.45096384
## P11554_214 0.003077474 -1.09285308
## P11554_215 -0.841447762 -0.65610279
## P11554_216 0.168941182 0.51634266
## P11554_217 0.359879450 0.56889672
## P11554_218 0.555484511 1.38379798
## P11554_225 -0.198144829 -1.73009069
## P11554_226 -0.623235407 0.29499499
## P11554_227 -0.152939586 0.02147920
## P11554_228 0.851545268 -0.08320649
## P11554_229 0.771180110 0.94776470
## P11554_230 2.277749579 1.15816323
##
## $`GO:0051301`$rowDendrogram
## 'dendrogram' with 2 branches and 74 members total, at height 3.824561
##
## $`GO:0051301`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0051301`$breaks
## [1] -4.00693843 -3.92679966 -3.84666089 -3.76652212 -3.68638335 -3.60624458
## [7] -3.52610582 -3.44596705 -3.36582828 -3.28568951 -3.20555074 -3.12541197
## [13] -3.04527320 -2.96513444 -2.88499567 -2.80485690 -2.72471813 -2.64457936
## [19] -2.56444059 -2.48430182 -2.40416306 -2.32402429 -2.24388552 -2.16374675
## [25] -2.08360798 -2.00346921 -1.92333044 -1.84319168 -1.76305291 -1.68291414
## [31] -1.60277537 -1.52263660 -1.44249783 -1.36235907 -1.28222030 -1.20208153
## [37] -1.12194276 -1.04180399 -0.96166522 -0.88152645 -0.80138769 -0.72124892
## [43] -0.64111015 -0.56097138 -0.48083261 -0.40069384 -0.32055507 -0.24041631
## [49] -0.16027754 -0.08013877 0.00000000 0.08013877 0.16027754 0.24041631
## [55] 0.32055507 0.40069384 0.48083261 0.56097138 0.64111015 0.72124892
## [61] 0.80138769 0.88152645 0.96166522 1.04180399 1.12194276 1.20208153
## [67] 1.28222030 1.36235907 1.44249783 1.52263660 1.60277537 1.68291414
## [73] 1.76305291 1.84319168 1.92333044 2.00346921 2.08360798 2.16374675
## [79] 2.24388552 2.32402429 2.40416306 2.48430182 2.56444059 2.64457936
## [85] 2.72471813 2.80485690 2.88499567 2.96513444 3.04527320 3.12541197
## [91] 3.20555074 3.28568951 3.36582828 3.44596705 3.52610582 3.60624458
## [97] 3.68638335 3.76652212 3.84666089 3.92679966 4.00693843
##
## $`GO:0051301`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0051301`$colorTable
## low high color
## 1 -4.00693843 -3.92679966 #0000FF
## 2 -3.92679966 -3.84666089 #0505FF
## 3 -3.84666089 -3.76652212 #0A0AFF
## 4 -3.76652212 -3.68638335 #0F0FFF
## 5 -3.68638335 -3.60624458 #1414FF
## 6 -3.60624458 -3.52610582 #1919FF
## 7 -3.52610582 -3.44596705 #1E1EFF
## 8 -3.44596705 -3.36582828 #2424FF
## 9 -3.36582828 -3.28568951 #2929FF
## 10 -3.28568951 -3.20555074 #2E2EFF
## 11 -3.20555074 -3.12541197 #3333FF
## 12 -3.12541197 -3.04527320 #3838FF
## 13 -3.04527320 -2.96513444 #3D3DFF
## 14 -2.96513444 -2.88499567 #4242FF
## 15 -2.88499567 -2.80485690 #4848FF
## 16 -2.80485690 -2.72471813 #4D4DFF
## 17 -2.72471813 -2.64457936 #5252FF
## 18 -2.64457936 -2.56444059 #5757FF
## 19 -2.56444059 -2.48430182 #5C5CFF
## 20 -2.48430182 -2.40416306 #6161FF
## 21 -2.40416306 -2.32402429 #6767FF
## 22 -2.32402429 -2.24388552 #6C6CFF
## 23 -2.24388552 -2.16374675 #7171FF
## 24 -2.16374675 -2.08360798 #7676FF
## 25 -2.08360798 -2.00346921 #7B7BFF
## 26 -2.00346921 -1.92333044 #8080FF
## 27 -1.92333044 -1.84319168 #8585FF
## 28 -1.84319168 -1.76305291 #8B8BFF
## 29 -1.76305291 -1.68291414 #9090FF
## 30 -1.68291414 -1.60277537 #9595FF
## 31 -1.60277537 -1.52263660 #9A9AFF
## 32 -1.52263660 -1.44249783 #9F9FFF
## 33 -1.44249783 -1.36235907 #A4A4FF
## 34 -1.36235907 -1.28222030 #AAAAFF
## 35 -1.28222030 -1.20208153 #AFAFFF
## 36 -1.20208153 -1.12194276 #B4B4FF
## 37 -1.12194276 -1.04180399 #B9B9FF
## 38 -1.04180399 -0.96166522 #BEBEFF
## 39 -0.96166522 -0.88152645 #C3C3FF
## 40 -0.88152645 -0.80138769 #C8C8FF
## 41 -0.80138769 -0.72124892 #CECEFF
## 42 -0.72124892 -0.64111015 #D3D3FF
## 43 -0.64111015 -0.56097138 #D8D8FF
## 44 -0.56097138 -0.48083261 #DDDDFF
## 45 -0.48083261 -0.40069384 #E2E2FF
## 46 -0.40069384 -0.32055507 #E7E7FF
## 47 -0.32055507 -0.24041631 #ECECFF
## 48 -0.24041631 -0.16027754 #F2F2FF
## 49 -0.16027754 -0.08013877 #F7F7FF
## 50 -0.08013877 0.00000000 #FCFCFF
## 51 0.00000000 0.08013877 #FFFCFC
## 52 0.08013877 0.16027754 #FFF7F7
## 53 0.16027754 0.24041631 #FFF2F2
## 54 0.24041631 0.32055507 #FFECEC
## 55 0.32055507 0.40069384 #FFE7E7
## 56 0.40069384 0.48083261 #FFE2E2
## 57 0.48083261 0.56097138 #FFDDDD
## 58 0.56097138 0.64111015 #FFD8D8
## 59 0.64111015 0.72124892 #FFD3D3
## 60 0.72124892 0.80138769 #FFCECE
## 61 0.80138769 0.88152645 #FFC8C8
## 62 0.88152645 0.96166522 #FFC3C3
## 63 0.96166522 1.04180399 #FFBEBE
## 64 1.04180399 1.12194276 #FFB9B9
## 65 1.12194276 1.20208153 #FFB4B4
## 66 1.20208153 1.28222030 #FFAFAF
## 67 1.28222030 1.36235907 #FFA9A9
## 68 1.36235907 1.44249783 #FFA4A4
## 69 1.44249783 1.52263660 #FF9F9F
## 70 1.52263660 1.60277537 #FF9A9A
## 71 1.60277537 1.68291414 #FF9595
## 72 1.68291414 1.76305291 #FF9090
## 73 1.76305291 1.84319168 #FF8B8B
## 74 1.84319168 1.92333044 #FF8585
## 75 1.92333044 2.00346921 #FF8080
## 76 2.00346921 2.08360798 #FF7B7B
## 77 2.08360798 2.16374675 #FF7676
## 78 2.16374675 2.24388552 #FF7171
## 79 2.24388552 2.32402429 #FF6C6C
## 80 2.32402429 2.40416306 #FF6767
## 81 2.40416306 2.48430182 #FF6161
## 82 2.48430182 2.56444059 #FF5C5C
## 83 2.56444059 2.64457936 #FF5757
## 84 2.64457936 2.72471813 #FF5252
## 85 2.72471813 2.80485690 #FF4D4D
## 86 2.80485690 2.88499567 #FF4848
## 87 2.88499567 2.96513444 #FF4242
## 88 2.96513444 3.04527320 #FF3D3D
## 89 3.04527320 3.12541197 #FF3838
## 90 3.12541197 3.20555074 #FF3333
## 91 3.20555074 3.28568951 #FF2E2E
## 92 3.28568951 3.36582828 #FF2929
## 93 3.36582828 3.44596705 #FF2424
## 94 3.44596705 3.52610582 #FF1E1E
## 95 3.52610582 3.60624458 #FF1919
## 96 3.60624458 3.68638335 #FF1414
## 97 3.68638335 3.76652212 #FF0F0F
## 98 3.76652212 3.84666089 #FF0A0A
## 99 3.84666089 3.92679966 #FF0505
## 100 3.92679966 4.00693843 #FF0000
##
## $`GO:0051301`$layout
## $`GO:0051301`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0051301`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0051301`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0007267`
## $`GO:0007267`$rowInd
## [1] 32 65 54 62 44 48 61 9 49 35 40 47 41 4 14 68 50 5 29 13 2 23 33 21 24
## [26] 80 77 52 10 45 75 7 20 72 30 15 66 78 22 70 25 38 57 79 73 71 36 27 37 6
## [51] 26 11 67 63 8 58 17 64 43 60 34 46 42 12 18 3 1 55 51 69 39 76 19 74 59
## [76] 56 16 31 53 28
##
## $`GO:0007267`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0007267`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0007267`$carpet
## AT2G31320 AT4G20910 AT3G60740 AT4G13950 AT3G16570 AT3G24340
## P11554_207 0.6746070 0.2286444 0.3625955 0.14409413 0.8195648 1.1675162
## P11554_208 0.7602131 0.9364704 1.0187156 0.82870040 1.0071569 1.0595894
## P11554_209 1.4915479 0.7384526 1.3197268 0.60173582 0.5956243 -0.1304834
## P11554_210 -1.7181133 -1.1259642 -0.9446227 -0.91892647 -0.9785436 -0.6868862
## P11554_211 -0.5416318 -0.6422914 -1.1135566 -0.93234417 -0.7939924 0.2596507
## P11554_212 -0.2930092 -0.5604655 -0.2542039 -1.32500925 -1.2584199 0.5041160
## P11554_213 2.0062609 1.2835512 0.5266130 -0.01348407 0.3421364 0.9357344
## P11554_214 0.9813375 0.7781553 0.4465593 0.39388985 0.4486510 0.4900528
## P11554_215 1.1176996 0.9060881 0.4421321 0.25130068 0.0877192 0.7741082
## P11554_216 -1.6263809 -1.6546271 -1.3489987 -0.42761550 -0.6746407 0.2910721
## P11554_217 -0.4775084 -1.4122696 -0.9891169 -0.81764221 -0.7464342 -1.8138943
## P11554_218 -0.9091896 -1.4278292 -0.5555976 -0.73049843 -1.2361606 -0.1168626
## P11554_225 -0.2039350 0.8962905 0.9590563 2.22960990 1.6106571 0.4384562
## P11554_226 -0.1909670 0.9466315 1.4552357 1.44944686 1.4129988 1.0144006
## P11554_227 0.0143302 0.9394540 1.4528621 1.44866569 1.5147696 0.2873560
## P11554_228 -0.3172102 0.4817486 -1.2997539 -0.56255455 -0.1762088 -0.8461378
## P11554_229 -0.3936088 -0.7306285 -1.0418753 -0.63759883 -1.1528501 -1.8138943
## P11554_230 -0.3744421 -0.5814111 -0.4357708 -0.98176984 -0.8220279 -1.8138943
## AT4G12970 AT1G23147 AT3G25170 AT2G33130 AT3G04735 AT3G23805
## P11554_207 -0.2357023 2.6528377 -0.2357023 -0.343577 -0.2357023 0.248820580
## P11554_208 4.0069384 -0.4296998 -0.2357023 -0.343577 -0.2357023 0.336926186
## P11554_209 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -1.012402991
## P11554_210 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -1.071170873
## P11554_211 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -1.117526664
## P11554_212 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -1.750210623
## P11554_213 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 1.205236032
## P11554_214 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 1.617577307
## P11554_215 -0.2357023 -0.4296998 -0.2357023 -0.343577 4.0069384 1.734575645
## P11554_216 -0.2357023 1.8777752 -0.2357023 -0.343577 -0.2357023 0.748884489
## P11554_217 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -0.582103801
## P11554_218 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 0.003700231
## P11554_225 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 0.823986177
## P11554_226 -0.2357023 1.9148846 4.0069384 2.776016 -0.2357023 0.607707679
## P11554_227 -0.2357023 -0.4296998 -0.2357023 2.721216 -0.2357023 0.142658003
## P11554_228 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -0.792707491
## P11554_229 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -0.646810575
## P11554_230 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -0.497139310
## AT3G05490 AT1G13220 AT1G48410 AT4G32551 AT3G28730 AT1G14690
## P11554_207 -0.5697022 0.2237902 -1.52185850 -0.24586246 -0.13054870 0.1659207
## P11554_208 -0.3459588 0.4242057 0.05451137 -0.02343463 0.19426429 1.1852905
## P11554_209 -0.7734944 -0.5970388 0.29427536 1.24411664 1.06469143 0.9232878
## P11554_210 -0.3583740 -0.2763459 -1.20210992 -1.44750996 -0.55302107 -0.2433289
## P11554_211 -0.6200579 -0.5645592 -1.01390535 -0.96563300 -0.77290097 -0.2492209
## P11554_212 -0.9016876 -0.9125255 -0.17301048 -1.40266329 0.52339236 -0.2134631
## P11554_213 1.3590096 1.7436094 0.48140777 0.55744855 1.15459167 0.9463752
## P11554_214 1.7292348 1.6056486 0.93994463 -0.33049464 0.42138809 1.1691222
## P11554_215 1.9205177 1.9126058 0.46290840 1.41713729 1.57421692 0.5451309
## P11554_216 0.9924449 0.8413009 0.73776929 0.60384180 -1.59885563 0.8784796
## P11554_217 0.9792312 -0.2281249 1.72800670 -0.35985219 -0.16269951 1.0294652
## P11554_218 0.6875802 0.5902724 1.12843318 0.75311016 0.01480992 1.0213956
## P11554_225 -0.3064405 -0.4577976 -1.93815311 -1.04945055 -1.77644692 -0.9828624
## P11554_226 -0.7251219 -0.6996219 -0.82091856 1.10591582 -0.26071494 -1.1338511
## P11554_227 -0.3058800 -0.9876139 0.47505566 0.96265526 -0.90377567 -1.2826664
## P11554_228 -0.8734185 -0.5523965 -0.70839668 -1.78357653 -0.66735898 -1.8212926
## P11554_229 -0.4796253 -1.6194727 0.20531390 0.41395223 -0.01222251 -1.0745297
## P11554_230 -1.4082571 -0.4459360 0.87072635 0.55029948 1.89119023 -0.8632526
## AT2G25420 AT1G34355 AT1G02900 AT1G72970 AT2G31970
## P11554_207 0.53170106 0.24804861 0.42872359 1.19550158 0.51952604
## P11554_208 0.95277411 0.41249520 -0.05431102 0.32431449 1.30550584
## P11554_209 0.63944597 -0.01991303 0.12455107 -0.01369041 0.80285990
## P11554_210 0.28796548 0.64174815 -0.34224203 0.97357155 0.21256270
## P11554_211 -0.02887163 0.48999551 -0.24271767 1.27102720 0.56207816
## P11554_212 -0.21990657 0.92099743 -0.35183374 -0.51475806 1.20296068
## P11554_213 0.68556765 0.95520235 0.73315926 1.40134628 0.98678503
## P11554_214 1.00023712 0.45922760 0.36631416 0.99313853 0.95922779
## P11554_215 1.67351025 0.69784078 1.95440748 1.20005183 0.70916466
## P11554_216 0.25101189 1.36247064 0.33591095 0.47499530 0.05033542
## P11554_217 0.30041623 0.91982736 1.59375858 -0.75317440 -0.17523484
## P11554_218 1.01704981 0.69497838 1.30443338 -0.44955327 0.39014806
## P11554_225 -0.56720161 -1.05633582 -1.18390541 -0.45837801 -1.75119982
## P11554_226 -1.37275710 -1.72969005 -1.93497142 -1.07728135 -1.48056476
## P11554_227 -0.76376557 -1.32848374 -0.44951498 -1.28696075 -0.79919408
## P11554_228 -1.51796106 -1.35965654 -1.37623412 -1.32062972 -1.12394590
## P11554_229 -0.88696620 -0.94739114 -0.46319748 -0.45012203 -1.28324758
## P11554_230 -1.98224981 -1.36136171 -0.44233061 -1.50939877 -1.08776731
## AT1G63640 AT1G77720 AT5G67070 AT5G35930 AT3G49250
## P11554_207 0.65362148 0.97425879 0.348571889 -0.2550288 0.76182230
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## P11554_209 0.66940459 0.89830918 0.225627566 0.1649827 0.76986399
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## P11554_212 0.41654947 0.33677735 -0.631480842 0.1016979 -0.37966898
## P11554_213 1.36595007 1.26326310 1.835577361 1.4210169 1.28148975
## P11554_214 1.35216418 1.59378183 1.671862472 1.7256504 1.75177795
## P11554_215 1.42003958 1.43112268 1.797836059 1.8317097 1.31526822
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## AT1G26540 AT3G20010 AT5G23880 AT1G18450 AT1G63470
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## P11554_208 0.93587684 0.94266435 0.91042166 1.1631874 0.72631587
## P11554_209 0.95170879 1.37792033 1.23114395 1.0523593 0.78423093
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## P11554_213 1.53455025 1.23990884 1.33242798 1.1999075 1.12779060
## P11554_214 1.72236590 1.53968926 1.39493209 1.2799718 1.45144030
## P11554_215 1.76972728 1.44631677 1.65436121 1.6818944 2.39794751
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## AT5G13000 AT2G27040 AT1G52310 AT4G30130 AT5G43810
## P11554_207 0.5290992 0.41763475 0.3347911 1.2209651 1.078106753
## P11554_208 0.8678384 0.80432846 1.1593615 2.0888481 1.293367617
## P11554_209 0.8735574 0.97810208 0.1920263 0.3744631 1.637428463
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## P11554_213 1.5463975 1.79610316 1.0279786 0.8988833 0.482358113
## P11554_214 1.8885572 1.49547662 0.9177961 0.6269807 1.275407582
## P11554_215 1.7481533 1.67298644 1.4121368 0.6989575 0.265311577
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## P11554_229 -1.4099146 -1.09200549 -1.3909118 -1.3721170 -0.848652249
## P11554_230 -0.7516615 -1.53499634 -0.4353509 -0.7983579 -1.151661491
## AT1G67720 AT5G02520 AT1G79950 AT2G47230 AT4G02460 AT5G63960
## P11554_207 2.26994666 1.3095250 1.0202117 1.1782779 1.1040710 1.1713245
## P11554_208 1.08273076 1.3714185 1.3262327 1.2746736 1.1458063 1.4549063
## P11554_209 0.85686673 1.3639613 1.2747931 1.1717015 1.5061699 1.2718754
## P11554_210 -0.38813020 -0.5063147 -0.5933934 -0.6616361 -0.2466275 -0.4380328
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## P11554_213 1.07719461 1.1536365 1.4788413 1.5551862 1.3806348 1.3679954
## P11554_214 0.90913832 1.1323069 1.4565954 1.4495981 1.3223978 1.3458729
## P11554_215 0.32330415 1.5778187 1.3275226 1.4838396 1.4811517 1.3777394
## P11554_216 -0.53274518 -0.5578037 -0.4289616 -0.4404988 -0.6866920 -0.7198209
## P11554_217 -0.04633694 -0.3368507 -0.5091918 -0.6088417 -0.4625901 -0.6517789
## P11554_218 -0.89249312 -0.8315809 -0.6039719 -0.6391131 -0.5323456 -0.5775556
## P11554_225 -0.09210698 -0.8509071 -0.5086952 -0.7398462 -0.9644814 -0.8001198
## P11554_226 0.66491493 -0.6355880 -0.6626215 -0.6015085 -0.9143301 -0.7574147
## P11554_227 -0.42442069 -0.5099174 -0.1849924 -0.5664692 -0.5973125 -0.4070590
## P11554_228 -1.69863481 -0.9570335 -1.0423317 -0.8885405 -1.2898066 -1.1241694
## P11554_229 -1.43825937 -1.3228988 -1.1100756 -1.0595206 -0.7971661 -1.0238247
## P11554_230 -0.29836864 -0.9443836 -1.3553116 -0.9248649 -0.8471189 -0.9988476
## AT5G13960 AT5G07660 AT2G39810 AT2G04660 AT2G41500 AT1G15940
## P11554_207 1.0043766 1.2489549 1.0190973 1.07739255 0.05371391 0.66447219
## P11554_208 1.3085413 1.5530785 1.0574856 1.20933328 0.63243545 1.09904282
## P11554_209 1.4788660 1.0678267 1.3057022 0.97961431 1.37934650 1.25457761
## P11554_210 -0.5948637 -0.5562306 -0.9499288 -0.52168925 -1.04871269 -0.48621910
## P11554_211 -0.3661511 -0.5788684 -0.7452699 -0.14361329 -0.73102220 -0.63116509
## P11554_212 -0.2414945 -0.3248160 -0.4641232 -0.29296701 -0.60359012 -0.15017172
## P11554_213 1.4390728 1.5205099 1.4202017 1.86541622 1.97365889 1.53815073
## P11554_214 1.2730129 1.1882190 1.3839114 1.23090727 1.59371631 1.70173669
## P11554_215 1.2866363 1.5131207 1.5140591 1.09795206 1.48405688 1.33385521
## P11554_216 -0.4534059 -0.7627030 -0.9580326 -0.57384071 -0.23238575 -0.67153976
## P11554_217 -0.4221551 -0.8524258 -0.7126134 -0.67491146 -0.44776873 -0.30835143
## P11554_218 -0.1337019 -0.6409672 -0.7614616 -0.89260216 -0.61728952 -0.35735464
## P11554_225 -0.8574390 -0.8694127 0.1506114 -0.28921836 0.04505351 -1.36329774
## P11554_226 -0.7709018 -0.4358695 -0.2219320 -0.11901983 -0.25208271 -1.08610872
## P11554_227 -0.3838525 -0.7069094 0.0375305 -0.06899327 -0.46384018 -1.17670938
## P11554_228 -1.3729869 -1.0280267 -0.9523112 -1.20870403 -1.25230610 -0.61176411
## P11554_229 -0.9757506 -0.7422745 -1.0881668 -1.57735310 -1.21976551 -0.77881942
## P11554_230 -1.2178030 -0.5932058 -1.0347599 -1.09770322 -0.29321794 0.02966586
## AT1G80070 AT1G28270 AT4G30520 AT4G14010 AT1G23145 AT4G02680
## P11554_207 -0.01727095 -1.1203284 -1.23792720 0.05533561 -0.6660491 -1.3308708
## P11554_208 1.01597205 1.3615340 0.19192144 -0.29840188 -0.6660491 -0.6491262
## P11554_209 1.60394095 -1.1203284 0.11025213 -0.18371571 -0.6660491 -0.4068994
## P11554_210 -0.57861865 -1.1203284 0.67224206 -0.25403005 -0.6660491 -0.5736486
## P11554_211 -0.60856498 0.6094841 1.67392327 0.79361513 -0.6660491 0.3698936
## P11554_212 0.14364166 -1.1203284 1.29726468 0.12178932 -0.6660491 0.2498876
## P11554_213 0.99648996 -1.1203284 -0.69066438 -1.50142413 -0.6660491 0.6474680
## P11554_214 1.82558364 0.2389941 0.72838307 -1.50142413 1.0496459 0.3597557
## P11554_215 1.29034482 0.8509567 -0.66149251 0.52479243 -0.6660491 1.1507537
## P11554_216 -0.48663979 1.2838196 0.14370403 1.57951215 1.0863126 1.0755470
## P11554_217 0.04434975 0.2282866 0.45689574 0.45874245 1.7409211 2.0377186
## P11554_218 -0.54038401 0.1719422 0.31787870 0.03236878 -0.6660491 0.8150792
## P11554_225 -1.03205865 0.5950864 -0.34597774 0.53443422 -0.6660491 -0.2395097
## P11554_226 -0.65672229 0.2903729 -0.75856714 -1.50142413 1.1144946 -1.6982802
## P11554_227 -0.35059283 1.6505050 1.48977335 1.09847739 -0.6660491 -1.6565144
## P11554_228 -1.86238034 -1.1203284 -1.35248031 -1.50142413 0.9446569 -0.3695215
## P11554_229 -1.00591506 0.5613169 -0.04506474 -0.08993208 -0.6660491 -0.3498109
## P11554_230 0.21882473 -1.1203284 -1.99006447 1.63270874 2.0565580 0.5680783
## AT1G59750 AT4G15800 AT3G14980 AT4G11510 AT2G32835 AT3G20550
## P11554_207 -1.87160109 -1.1441945 -0.75328798 -0.7613177 -0.4235532 -0.02832461
## P11554_208 -1.14276650 -1.7336564 -2.16952776 -0.7613177 -0.4235532 -0.19259560
## P11554_209 -1.11498420 -1.3176481 -0.64747997 -0.7613177 -0.4235532 0.18075744
## P11554_210 -1.07266336 0.2595927 -0.01768062 -0.7613177 -0.4235532 -2.08959079
## P11554_211 0.06430631 0.3124882 -0.02735611 -0.7613177 -0.4235532 0.10138744
## P11554_212 0.04093614 -0.2486275 -0.64207184 -0.7613177 -0.4235532 0.63839748
## P11554_213 1.25555904 0.3036502 0.08949454 1.5413474 -0.4235532 -1.47144133
## P11554_214 1.09188571 0.2649745 0.31484866 -0.7613177 -0.4235532 -1.05537712
## P11554_215 -0.62100893 0.7539593 0.03564527 -0.7613177 -0.4235532 -1.20715201
## P11554_216 1.17491283 1.6015125 1.64156328 -0.7613177 -0.4235532 -0.76730071
## P11554_217 1.73855466 1.6911603 1.68991240 -0.7613177 -0.4235532 -0.16309407
## P11554_218 1.32372677 1.5642912 1.87706075 1.2476238 -0.4235532 0.08426137
## P11554_225 0.34176729 -1.0389906 0.10943006 1.1245610 -0.4235532 0.67714673
## P11554_226 -0.32714803 -0.7009261 -0.39282264 0.7895675 -0.4235532 1.01441648
## P11554_227 -0.37352043 -0.7094689 -0.51441630 -0.7613177 2.3469110 0.94431463
## P11554_228 -0.26520763 0.1115789 0.58210573 1.6681699 1.3805054 0.77491213
## P11554_229 -0.02416369 0.1424487 -0.94147392 1.0874358 -0.4235532 0.76397012
## P11554_230 -0.21858489 -0.1121445 -0.23394353 0.9157893 2.6258815 1.79531244
## AT3G12550 AT1G32490 AT1G60860 AT1G10180 AT1G01040 AT3G61670
## P11554_207 -1.0572717 -1.0337991 -1.76418508 -1.07632503 -1.3115320 -1.5364060
## P11554_208 -0.2535475 -0.8426726 1.04476694 -1.65230820 -0.7744384 -0.9949497
## P11554_209 -0.6577436 -0.6610084 -1.04317608 -0.34094014 -1.4200139 -0.8775983
## P11554_210 -0.4421620 -0.5020562 -1.52609755 -0.70708499 0.8988952 0.9084578
## P11554_211 -0.7315885 -0.2281090 -0.80043708 0.79520028 0.7108268 1.2840130
## P11554_212 -0.1804889 0.4718843 0.04036054 1.46892388 0.6246917 1.3714980
## P11554_213 -0.5999747 -1.1902859 0.44329222 0.72878349 -1.2056908 -1.0765944
## P11554_214 -0.8573593 -1.4969458 0.24602003 0.20677914 -0.9238791 -1.1662484
## P11554_215 -0.7444723 -0.4244520 -0.51819749 -0.60893544 -0.9053433 -1.4403948
## P11554_216 -0.7790644 -0.7056244 -1.12831809 -0.11407172 0.7386751 1.0058127
## P11554_217 -1.0206630 -0.4977627 -0.63820830 -0.10497805 1.0933438 1.1213435
## P11554_218 -0.5888197 0.2255402 -0.23912672 0.72420135 1.1233242 0.9985261
## P11554_225 1.6501093 0.7981651 0.65532742 -2.04041059 -0.2724168 -0.1966739
## P11554_226 1.1370248 1.1794312 1.44164004 -0.48839423 -1.0592288 -0.0233746
## P11554_227 1.6514643 0.9984364 1.41305039 0.92970882 -0.1929106 -0.2175078
## P11554_228 0.9361267 1.0630809 0.74612759 -0.02270164 1.0072603 -0.1596830
## P11554_229 1.0083383 0.5811784 0.60332578 1.53492525 0.2873480 0.3378818
## P11554_230 1.5300921 2.2649995 1.02383544 0.76762782 1.5810886 0.6618980
## AT3G43920 AT5G02030 AT3G03300 AT5G25475 AT1G63020 AT5G20320
## P11554_207 -1.64727307 -0.6329378 -1.1671235 -1.6756594 -1.3923576 -1.4692329
## P11554_208 -0.91117855 -0.6179165 -1.2653635 -1.3156358 -1.0181246 -0.9562479
## P11554_209 -0.42900811 -0.3524780 -0.6917712 -1.5989665 -0.7121019 -0.9028566
## P11554_210 0.61625960 1.1595349 1.1788081 0.9298602 0.6103624 0.6202526
## P11554_211 1.07774021 1.3132091 0.4654904 -0.0113235 0.2657725 0.6407808
## P11554_212 1.04526891 1.1799659 1.3258134 0.6815380 0.5926986 1.0292892
## P11554_213 -1.66881669 -1.8140522 -1.9548990 -0.1574369 -1.5725624 -0.9746916
## P11554_214 -0.83540882 -1.6393306 -0.9409194 -1.4671597 -1.4162399 -1.4842077
## P11554_215 -1.38626714 -1.4745319 -0.8944204 -0.5528083 -1.6297587 -1.9204813
## P11554_216 0.86854066 0.8264781 1.0162407 0.9437296 0.2112635 0.0283223
## P11554_217 1.58115735 0.7574347 0.7773962 0.6885873 0.2894457 0.4515604
## P11554_218 0.90555754 0.5978811 0.5489988 1.5370129 0.2331141 0.2723480
## P11554_225 -0.12680717 -0.2084781 -0.7304137 -0.6195375 0.8787729 0.2929101
## P11554_226 -0.17036943 -0.4786688 0.3056770 0.1498166 0.8898291 0.5427557
## P11554_227 -0.30558078 -0.5550081 -0.2577524 0.6026779 1.1645799 0.8616291
## P11554_228 -0.02024755 0.5059021 0.3922378 0.5309910 0.5338681 0.7763242
## P11554_229 0.57803997 0.7481412 0.7098016 1.1273434 1.2014328 1.1669007
## P11554_230 0.82839307 0.6848550 1.1821991 0.2069706 0.8700056 1.0246448
## AT4G11130 AT4G02020 AT1G54490 AT2G28290 AT3G57300
## P11554_207 -1.20817116 -1.14609778 -1.54786562 -1.598407729 -1.49453637
## P11554_208 -0.29313899 -0.47259664 -1.19977274 -0.897973326 -1.00256764
## P11554_209 -0.80268859 -0.50897021 -0.60761995 -0.729718839 -1.45820264
## P11554_210 0.26695250 0.78813996 0.47977619 -0.225498472 -0.17884559
## P11554_211 0.59170956 0.64923294 0.70415571 0.009059281 0.06271207
## P11554_212 1.09483597 1.30865112 1.02374449 0.652195899 0.80173130
## P11554_213 -1.60393167 -1.20049158 -1.46135676 -1.303445640 -1.29449428
## P11554_214 -1.22732848 -1.74610465 -0.94449463 -0.739814054 -0.68609147
## P11554_215 -1.92313413 -1.97235879 -0.97350789 -1.362540984 -1.22687775
## P11554_216 0.07155204 -0.10222851 -0.19211720 0.114598826 -0.05185905
## P11554_217 -0.01775822 0.22610203 0.06983100 0.600958661 0.22925493
## P11554_218 -0.22752745 -0.03638426 0.23425133 0.324075474 0.54040959
## P11554_225 0.46684278 0.31851912 -0.33571819 -0.064865493 0.16559213
## P11554_226 0.71905725 0.10888412 0.05210359 0.108255228 0.60186398
## P11554_227 0.54404742 0.63964037 0.43097040 0.685340782 1.14351103
## P11554_228 1.34182452 1.19356631 1.13749573 0.948210616 1.08578207
## P11554_229 1.31423443 0.70011703 1.08784197 1.187784646 1.01731193
## P11554_230 0.89262221 1.25237943 2.04228257 2.291785125 1.74530575
## AT2G16390
## P11554_207 -1.7937118
## P11554_208 -0.5709286
## P11554_209 -0.9449207
## P11554_210 0.4052434
## P11554_211 1.0841476
## P11554_212 0.4029780
## P11554_213 -1.4020702
## P11554_214 -1.3283511
## P11554_215 -0.9859428
## P11554_216 -0.5137124
## P11554_217 0.7448645
## P11554_218 0.8953971
## P11554_225 0.7447231
## P11554_226 0.5487191
## P11554_227 -0.2891289
## P11554_228 1.2543943
## P11554_229 0.2834583
## P11554_230 1.4648410
##
## $`GO:0007267`$rowDendrogram
## 'dendrogram' with 2 branches and 80 members total, at height 3.839715
##
## $`GO:0007267`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0007267`$breaks
## [1] -4.00693843 -3.92679966 -3.84666089 -3.76652212 -3.68638335 -3.60624458
## [7] -3.52610582 -3.44596705 -3.36582828 -3.28568951 -3.20555074 -3.12541197
## [13] -3.04527320 -2.96513444 -2.88499567 -2.80485690 -2.72471813 -2.64457936
## [19] -2.56444059 -2.48430182 -2.40416306 -2.32402429 -2.24388552 -2.16374675
## [25] -2.08360798 -2.00346921 -1.92333044 -1.84319168 -1.76305291 -1.68291414
## [31] -1.60277537 -1.52263660 -1.44249783 -1.36235907 -1.28222030 -1.20208153
## [37] -1.12194276 -1.04180399 -0.96166522 -0.88152645 -0.80138769 -0.72124892
## [43] -0.64111015 -0.56097138 -0.48083261 -0.40069384 -0.32055507 -0.24041631
## [49] -0.16027754 -0.08013877 0.00000000 0.08013877 0.16027754 0.24041631
## [55] 0.32055507 0.40069384 0.48083261 0.56097138 0.64111015 0.72124892
## [61] 0.80138769 0.88152645 0.96166522 1.04180399 1.12194276 1.20208153
## [67] 1.28222030 1.36235907 1.44249783 1.52263660 1.60277537 1.68291414
## [73] 1.76305291 1.84319168 1.92333044 2.00346921 2.08360798 2.16374675
## [79] 2.24388552 2.32402429 2.40416306 2.48430182 2.56444059 2.64457936
## [85] 2.72471813 2.80485690 2.88499567 2.96513444 3.04527320 3.12541197
## [91] 3.20555074 3.28568951 3.36582828 3.44596705 3.52610582 3.60624458
## [97] 3.68638335 3.76652212 3.84666089 3.92679966 4.00693843
##
## $`GO:0007267`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0007267`$colorTable
## low high color
## 1 -4.00693843 -3.92679966 #0000FF
## 2 -3.92679966 -3.84666089 #0505FF
## 3 -3.84666089 -3.76652212 #0A0AFF
## 4 -3.76652212 -3.68638335 #0F0FFF
## 5 -3.68638335 -3.60624458 #1414FF
## 6 -3.60624458 -3.52610582 #1919FF
## 7 -3.52610582 -3.44596705 #1E1EFF
## 8 -3.44596705 -3.36582828 #2424FF
## 9 -3.36582828 -3.28568951 #2929FF
## 10 -3.28568951 -3.20555074 #2E2EFF
## 11 -3.20555074 -3.12541197 #3333FF
## 12 -3.12541197 -3.04527320 #3838FF
## 13 -3.04527320 -2.96513444 #3D3DFF
## 14 -2.96513444 -2.88499567 #4242FF
## 15 -2.88499567 -2.80485690 #4848FF
## 16 -2.80485690 -2.72471813 #4D4DFF
## 17 -2.72471813 -2.64457936 #5252FF
## 18 -2.64457936 -2.56444059 #5757FF
## 19 -2.56444059 -2.48430182 #5C5CFF
## 20 -2.48430182 -2.40416306 #6161FF
## 21 -2.40416306 -2.32402429 #6767FF
## 22 -2.32402429 -2.24388552 #6C6CFF
## 23 -2.24388552 -2.16374675 #7171FF
## 24 -2.16374675 -2.08360798 #7676FF
## 25 -2.08360798 -2.00346921 #7B7BFF
## 26 -2.00346921 -1.92333044 #8080FF
## 27 -1.92333044 -1.84319168 #8585FF
## 28 -1.84319168 -1.76305291 #8B8BFF
## 29 -1.76305291 -1.68291414 #9090FF
## 30 -1.68291414 -1.60277537 #9595FF
## 31 -1.60277537 -1.52263660 #9A9AFF
## 32 -1.52263660 -1.44249783 #9F9FFF
## 33 -1.44249783 -1.36235907 #A4A4FF
## 34 -1.36235907 -1.28222030 #AAAAFF
## 35 -1.28222030 -1.20208153 #AFAFFF
## 36 -1.20208153 -1.12194276 #B4B4FF
## 37 -1.12194276 -1.04180399 #B9B9FF
## 38 -1.04180399 -0.96166522 #BEBEFF
## 39 -0.96166522 -0.88152645 #C3C3FF
## 40 -0.88152645 -0.80138769 #C8C8FF
## 41 -0.80138769 -0.72124892 #CECEFF
## 42 -0.72124892 -0.64111015 #D3D3FF
## 43 -0.64111015 -0.56097138 #D8D8FF
## 44 -0.56097138 -0.48083261 #DDDDFF
## 45 -0.48083261 -0.40069384 #E2E2FF
## 46 -0.40069384 -0.32055507 #E7E7FF
## 47 -0.32055507 -0.24041631 #ECECFF
## 48 -0.24041631 -0.16027754 #F2F2FF
## 49 -0.16027754 -0.08013877 #F7F7FF
## 50 -0.08013877 0.00000000 #FCFCFF
## 51 0.00000000 0.08013877 #FFFCFC
## 52 0.08013877 0.16027754 #FFF7F7
## 53 0.16027754 0.24041631 #FFF2F2
## 54 0.24041631 0.32055507 #FFECEC
## 55 0.32055507 0.40069384 #FFE7E7
## 56 0.40069384 0.48083261 #FFE2E2
## 57 0.48083261 0.56097138 #FFDDDD
## 58 0.56097138 0.64111015 #FFD8D8
## 59 0.64111015 0.72124892 #FFD3D3
## 60 0.72124892 0.80138769 #FFCECE
## 61 0.80138769 0.88152645 #FFC8C8
## 62 0.88152645 0.96166522 #FFC3C3
## 63 0.96166522 1.04180399 #FFBEBE
## 64 1.04180399 1.12194276 #FFB9B9
## 65 1.12194276 1.20208153 #FFB4B4
## 66 1.20208153 1.28222030 #FFAFAF
## 67 1.28222030 1.36235907 #FFA9A9
## 68 1.36235907 1.44249783 #FFA4A4
## 69 1.44249783 1.52263660 #FF9F9F
## 70 1.52263660 1.60277537 #FF9A9A
## 71 1.60277537 1.68291414 #FF9595
## 72 1.68291414 1.76305291 #FF9090
## 73 1.76305291 1.84319168 #FF8B8B
## 74 1.84319168 1.92333044 #FF8585
## 75 1.92333044 2.00346921 #FF8080
## 76 2.00346921 2.08360798 #FF7B7B
## 77 2.08360798 2.16374675 #FF7676
## 78 2.16374675 2.24388552 #FF7171
## 79 2.24388552 2.32402429 #FF6C6C
## 80 2.32402429 2.40416306 #FF6767
## 81 2.40416306 2.48430182 #FF6161
## 82 2.48430182 2.56444059 #FF5C5C
## 83 2.56444059 2.64457936 #FF5757
## 84 2.64457936 2.72471813 #FF5252
## 85 2.72471813 2.80485690 #FF4D4D
## 86 2.80485690 2.88499567 #FF4848
## 87 2.88499567 2.96513444 #FF4242
## 88 2.96513444 3.04527320 #FF3D3D
## 89 3.04527320 3.12541197 #FF3838
## 90 3.12541197 3.20555074 #FF3333
## 91 3.20555074 3.28568951 #FF2E2E
## 92 3.28568951 3.36582828 #FF2929
## 93 3.36582828 3.44596705 #FF2424
## 94 3.44596705 3.52610582 #FF1E1E
## 95 3.52610582 3.60624458 #FF1919
## 96 3.60624458 3.68638335 #FF1414
## 97 3.68638335 3.76652212 #FF0F0F
## 98 3.76652212 3.84666089 #FF0A0A
## 99 3.84666089 3.92679966 #FF0505
## 100 3.92679966 4.00693843 #FF0000
##
## $`GO:0007267`$layout
## $`GO:0007267`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0007267`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0007267`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0007017`
## $`GO:0007017`$rowInd
## [1] 17 14 9 16 21 6 13 1 20 8 18 2 4 7 3 19 15 5 12 11 10
##
## $`GO:0007017`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0007017`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0007017`$carpet
## AT5G12250 AT3G60740 AT2G35630 AT4G38950 AT5G48120
## P11554_207 1.01310448 0.3625955 0.1430261 0.61678989 0.927973362
## P11554_208 1.07728782 1.0187156 1.2003548 0.83278006 1.232566658
## P11554_209 1.74123425 1.3197268 0.6027948 1.36542957 1.457262303
## P11554_210 -0.22340226 -0.9446227 -1.1445314 -1.24378513 -0.634402768
## P11554_211 -0.05105366 -1.1135566 -0.8213790 -0.73763707 -0.284745361
## P11554_212 -0.15911724 -0.2542039 -0.5580962 -0.87837989 -0.591787979
## P11554_213 0.62819604 0.5266130 1.4564536 1.80827289 1.277558766
## P11554_214 0.94442155 0.4465593 1.8962345 1.45694180 1.072097161
## P11554_215 0.34820451 0.4421321 1.8502377 1.54499981 1.695682054
## P11554_216 -0.23399446 -1.3489987 -0.4144303 -0.05644639 -1.295595007
## P11554_217 -0.51877346 -0.9891169 -0.4645613 -0.58683798 -1.163376914
## P11554_218 -0.14546970 -0.5555976 -0.3899318 -0.73404987 -0.631159181
## P11554_225 -0.22207016 0.9590563 -0.4330152 -0.40960257 -0.785943232
## P11554_226 0.45539693 1.4552357 0.0371837 -0.14343372 -0.004303675
## P11554_227 0.40784419 1.4528621 -0.1109510 -0.36832104 0.028160499
## P11554_228 -2.43063000 -1.2997539 -1.1600034 -1.05341650 -0.902797509
## P11554_229 -1.03457418 -1.0418753 -1.1804531 -0.48234020 -0.986153867
## P11554_230 -1.59660466 -0.4357708 -0.5089325 -0.93096368 -0.411035314
## AT2G07170 AT3G57060 AT1G04820 AT5G23860 AT2G29550 AT5G19780
## P11554_207 1.16246877 0.9055023 0.3439908 0.3794242 0.1310512 0.3597171
## P11554_208 1.21521868 1.3248193 0.3992504 0.3432332 0.5708164 0.5490231
## P11554_209 1.21044060 1.2934175 0.4477707 0.5813971 0.7295304 0.6998046
## P11554_210 -0.66107760 -1.1210399 -0.6573452 -0.6536335 -0.7481668 -0.8258303
## P11554_211 -0.12282299 -0.3383086 -0.5259092 -0.5370360 -0.6784380 -0.6229056
## P11554_212 0.10803380 -0.1828023 -0.6861032 -0.7629816 -0.7691975 -0.8137399
## P11554_213 0.86065807 1.1779512 1.6479346 1.7189540 1.3343424 1.3895713
## P11554_214 1.47539009 1.7583214 1.7452839 1.7402803 1.6689398 1.5966033
## P11554_215 1.28567065 1.3730028 1.6742281 1.6000069 1.3170253 1.4907055
## P11554_216 -0.12647254 -0.9483376 0.5340004 0.3325845 0.6921219 0.6400695
## P11554_217 0.05602871 -0.1049427 0.4259223 0.3219671 0.7092924 0.6639006
## P11554_218 0.23599004 -0.5949872 0.4370309 0.3417132 0.7355537 0.5802608
## P11554_225 -1.08364674 -0.9290415 -0.7866537 -0.6710811 -0.6632016 -0.7295494
## P11554_226 -1.05232203 -0.7377822 -0.6266267 -0.3193042 -0.5748630 -0.5207351
## P11554_227 -1.13010657 -0.3559859 -0.6479091 -0.4295104 -0.4049358 -0.5089175
## P11554_228 -1.31162882 -0.9782933 -1.1997151 -1.3969466 -1.7149547 -1.6745996
## P11554_229 -1.24453093 -0.6305703 -1.0875526 -0.9878590 -0.9573779 -1.0773214
## P11554_230 -0.87729120 -0.9109230 -1.4375972 -1.6012080 -1.3775382 -1.1960571
## AT1G20010 AT1G50010 AT2G16960 AT1G23220 AT5G20110
## P11554_207 -0.01621384 0.5212103 0.7507300 -0.2313748 1.499764822
## P11554_208 0.15191099 0.5108780 0.2208699 0.6325258 0.615923003
## P11554_209 0.33565806 0.5196580 0.7572320 -0.3447339 0.169777905
## P11554_210 -0.81376750 -0.3956559 -0.1357354 -0.2074379 -1.363573565
## P11554_211 -0.71522624 -0.2533151 0.1263280 0.3899693 0.705472112
## P11554_212 -0.78642917 -0.5212547 0.8231631 1.6384612 1.307037129
## P11554_213 2.12449051 1.5085726 0.9788360 -0.1036907 -1.363573565
## P11554_214 1.89614734 1.5690105 0.4685176 -1.8915740 -0.035907254
## P11554_215 1.69347453 1.4904491 0.4421712 -0.3853606 -0.001959232
## P11554_216 0.07336438 0.6467112 1.2764184 -1.4456979 -1.363573565
## P11554_217 0.19750907 0.5674713 0.9886698 0.2919081 -0.046365419
## P11554_218 0.38793521 0.4246418 1.0017659 -0.1936652 1.457548933
## P11554_225 -0.41068444 -0.9400601 -1.2183806 -0.8145368 -1.363573565
## P11554_226 -0.45958671 -1.0765168 -1.2391764 -1.0745170 0.014274977
## P11554_227 -0.57921079 -0.9456320 -1.6126028 1.9807346 -0.009928913
## P11554_228 -0.96339097 -0.6757951 -1.4082173 -0.1537870 0.398952286
## P11554_229 -1.15287121 -1.2759311 -1.2680410 0.9149520 -1.363573565
## P11554_230 -0.96310921 -1.6744422 -0.9525483 0.9978245 0.743277476
## AT4G15930 AT1G64740 AT3G44200 AT3G16120 AT2G40730
## P11554_207 -1.75778025 -1.4735795 -1.3808606 -0.6650381 -2.96390603
## P11554_208 -1.69998416 -0.9793049 -1.1584601 -0.6650381 -0.77346157
## P11554_209 -1.18667540 -0.7892601 -0.8106267 1.2279407 0.15965364
## P11554_210 0.30117569 0.6477472 0.8489747 -0.6650381 -0.91593793
## P11554_211 -0.30803022 0.3964392 1.0436602 -0.6650381 -0.57073463
## P11554_212 0.24518634 0.5728144 1.2973551 2.1905559 0.51906288
## P11554_213 -0.85691659 -1.2854393 -1.5118129 -0.6650381 0.59355407
## P11554_214 -1.34159437 -1.4441564 -1.2193226 -0.6650381 0.33759844
## P11554_215 -0.39773970 -1.5797635 -1.0400561 -0.6650381 -0.27958572
## P11554_216 0.65066899 0.6993732 0.7539289 1.0090436 -0.18556597
## P11554_217 0.31150303 0.7384874 0.8060383 -0.6650381 0.26809029
## P11554_218 1.38024615 0.7407431 1.0893873 -0.6650381 -0.85226046
## P11554_225 0.88608121 -0.2168095 -0.4325019 -0.6650381 0.80488927
## P11554_226 0.97615339 0.3114415 -0.2556676 1.0359666 1.45089943
## P11554_227 1.00772118 0.1669480 -0.3683096 1.0060860 1.03489030
## P11554_228 0.06392309 0.7846254 0.8609064 1.5108649 0.47367036
## P11554_229 0.88801317 1.5368152 0.4922013 -0.6650381 0.04474284
## P11554_230 0.83804846 1.1728784 0.9851659 -0.6650381 0.85440078
##
## $`GO:0007017`$rowDendrogram
## 'dendrogram' with 2 branches and 21 members total, at height 1.984466
##
## $`GO:0007017`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0007017`$breaks
## [1] -2.96390603 -2.90462791 -2.84534979 -2.78607166 -2.72679354 -2.66751542
## [7] -2.60823730 -2.54895918 -2.48968106 -2.43040294 -2.37112482 -2.31184670
## [13] -2.25256858 -2.19329046 -2.13401234 -2.07473422 -2.01545610 -1.95617798
## [19] -1.89689986 -1.83762174 -1.77834362 -1.71906550 -1.65978737 -1.60050925
## [25] -1.54123113 -1.48195301 -1.42267489 -1.36339677 -1.30411865 -1.24484053
## [31] -1.18556241 -1.12628429 -1.06700617 -1.00772805 -0.94844993 -0.88917181
## [37] -0.82989369 -0.77061557 -0.71133745 -0.65205933 -0.59278121 -0.53350308
## [43] -0.47422496 -0.41494684 -0.35566872 -0.29639060 -0.23711248 -0.17783436
## [49] -0.11855624 -0.05927812 0.00000000 0.05927812 0.11855624 0.17783436
## [55] 0.23711248 0.29639060 0.35566872 0.41494684 0.47422496 0.53350308
## [61] 0.59278121 0.65205933 0.71133745 0.77061557 0.82989369 0.88917181
## [67] 0.94844993 1.00772805 1.06700617 1.12628429 1.18556241 1.24484053
## [73] 1.30411865 1.36339677 1.42267489 1.48195301 1.54123113 1.60050925
## [79] 1.65978737 1.71906550 1.77834362 1.83762174 1.89689986 1.95617798
## [85] 2.01545610 2.07473422 2.13401234 2.19329046 2.25256858 2.31184670
## [91] 2.37112482 2.43040294 2.48968106 2.54895918 2.60823730 2.66751542
## [97] 2.72679354 2.78607166 2.84534979 2.90462791 2.96390603
##
## $`GO:0007017`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0007017`$colorTable
## low high color
## 1 -2.96390603 -2.90462791 #0000FF
## 2 -2.90462791 -2.84534979 #0505FF
## 3 -2.84534979 -2.78607166 #0A0AFF
## 4 -2.78607166 -2.72679354 #0F0FFF
## 5 -2.72679354 -2.66751542 #1414FF
## 6 -2.66751542 -2.60823730 #1919FF
## 7 -2.60823730 -2.54895918 #1E1EFF
## 8 -2.54895918 -2.48968106 #2424FF
## 9 -2.48968106 -2.43040294 #2929FF
## 10 -2.43040294 -2.37112482 #2E2EFF
## 11 -2.37112482 -2.31184670 #3333FF
## 12 -2.31184670 -2.25256858 #3838FF
## 13 -2.25256858 -2.19329046 #3D3DFF
## 14 -2.19329046 -2.13401234 #4242FF
## 15 -2.13401234 -2.07473422 #4848FF
## 16 -2.07473422 -2.01545610 #4D4DFF
## 17 -2.01545610 -1.95617798 #5252FF
## 18 -1.95617798 -1.89689986 #5757FF
## 19 -1.89689986 -1.83762174 #5C5CFF
## 20 -1.83762174 -1.77834362 #6161FF
## 21 -1.77834362 -1.71906550 #6767FF
## 22 -1.71906550 -1.65978737 #6C6CFF
## 23 -1.65978737 -1.60050925 #7171FF
## 24 -1.60050925 -1.54123113 #7676FF
## 25 -1.54123113 -1.48195301 #7B7BFF
## 26 -1.48195301 -1.42267489 #8080FF
## 27 -1.42267489 -1.36339677 #8585FF
## 28 -1.36339677 -1.30411865 #8B8BFF
## 29 -1.30411865 -1.24484053 #9090FF
## 30 -1.24484053 -1.18556241 #9595FF
## 31 -1.18556241 -1.12628429 #9A9AFF
## 32 -1.12628429 -1.06700617 #9F9FFF
## 33 -1.06700617 -1.00772805 #A4A4FF
## 34 -1.00772805 -0.94844993 #AAAAFF
## 35 -0.94844993 -0.88917181 #AFAFFF
## 36 -0.88917181 -0.82989369 #B4B4FF
## 37 -0.82989369 -0.77061557 #B9B9FF
## 38 -0.77061557 -0.71133745 #BEBEFF
## 39 -0.71133745 -0.65205933 #C3C3FF
## 40 -0.65205933 -0.59278121 #C8C8FF
## 41 -0.59278121 -0.53350308 #CECEFF
## 42 -0.53350308 -0.47422496 #D3D3FF
## 43 -0.47422496 -0.41494684 #D8D8FF
## 44 -0.41494684 -0.35566872 #DDDDFF
## 45 -0.35566872 -0.29639060 #E2E2FF
## 46 -0.29639060 -0.23711248 #E7E7FF
## 47 -0.23711248 -0.17783436 #ECECFF
## 48 -0.17783436 -0.11855624 #F2F2FF
## 49 -0.11855624 -0.05927812 #F7F7FF
## 50 -0.05927812 0.00000000 #FCFCFF
## 51 0.00000000 0.05927812 #FFFCFC
## 52 0.05927812 0.11855624 #FFF7F7
## 53 0.11855624 0.17783436 #FFF2F2
## 54 0.17783436 0.23711248 #FFECEC
## 55 0.23711248 0.29639060 #FFE7E7
## 56 0.29639060 0.35566872 #FFE2E2
## 57 0.35566872 0.41494684 #FFDDDD
## 58 0.41494684 0.47422496 #FFD8D8
## 59 0.47422496 0.53350308 #FFD3D3
## 60 0.53350308 0.59278121 #FFCECE
## 61 0.59278121 0.65205933 #FFC8C8
## 62 0.65205933 0.71133745 #FFC3C3
## 63 0.71133745 0.77061557 #FFBEBE
## 64 0.77061557 0.82989369 #FFB9B9
## 65 0.82989369 0.88917181 #FFB4B4
## 66 0.88917181 0.94844993 #FFAFAF
## 67 0.94844993 1.00772805 #FFA9A9
## 68 1.00772805 1.06700617 #FFA4A4
## 69 1.06700617 1.12628429 #FF9F9F
## 70 1.12628429 1.18556241 #FF9A9A
## 71 1.18556241 1.24484053 #FF9595
## 72 1.24484053 1.30411865 #FF9090
## 73 1.30411865 1.36339677 #FF8B8B
## 74 1.36339677 1.42267489 #FF8585
## 75 1.42267489 1.48195301 #FF8080
## 76 1.48195301 1.54123113 #FF7B7B
## 77 1.54123113 1.60050925 #FF7676
## 78 1.60050925 1.65978737 #FF7171
## 79 1.65978737 1.71906550 #FF6C6C
## 80 1.71906550 1.77834362 #FF6767
## 81 1.77834362 1.83762174 #FF6161
## 82 1.83762174 1.89689986 #FF5C5C
## 83 1.89689986 1.95617798 #FF5757
## 84 1.95617798 2.01545610 #FF5252
## 85 2.01545610 2.07473422 #FF4D4D
## 86 2.07473422 2.13401234 #FF4848
## 87 2.13401234 2.19329046 #FF4242
## 88 2.19329046 2.25256858 #FF3D3D
## 89 2.25256858 2.31184670 #FF3838
## 90 2.31184670 2.37112482 #FF3333
## 91 2.37112482 2.43040294 #FF2E2E
## 92 2.43040294 2.48968106 #FF2929
## 93 2.48968106 2.54895918 #FF2424
## 94 2.54895918 2.60823730 #FF1E1E
## 95 2.60823730 2.66751542 #FF1919
## 96 2.66751542 2.72679354 #FF1414
## 97 2.72679354 2.78607166 #FF0F0F
## 98 2.78607166 2.84534979 #FF0A0A
## 99 2.84534979 2.90462791 #FF0505
## 100 2.90462791 2.96390603 #FF0000
##
## $`GO:0007017`$layout
## $`GO:0007017`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0007017`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0007017`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0040029`
## $`GO:0040029`$rowInd
## [1] 15 13 7 8 1 10 14 5 6 2 12 11 9 3 16 4
##
## $`GO:0040029`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0040029`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0040029`$carpet
## AT4G24680 AT4G13520 AT2G33290 AT2G33610 AT1G21700
## P11554_207 -1.3338652 -1.15305181 -0.2318041 -1.01014314 -1.69448212
## P11554_208 0.1148197 -0.32203614 -0.1709910 -1.15162864 -1.63937576
## P11554_209 0.7019795 -0.32606644 -0.0697298 0.07262426 -0.76212646
## P11554_210 -0.7712075 -0.45998475 -0.8836632 -0.95632623 0.04545705
## P11554_211 -0.7983743 -0.33953929 -1.0621427 -1.21305539 -0.03943629
## P11554_212 1.4439755 -0.70956695 -1.0682378 -0.49936206 1.52519342
## P11554_213 -0.3627378 -0.82044097 -0.4141906 0.10395548 -0.30324298
## P11554_214 0.6009217 -0.67218157 -0.1996269 -0.16601942 -0.54550476
## P11554_215 -1.0060776 -0.62897504 0.1696977 0.22666028 -0.13042670
## P11554_216 -0.9191117 -0.66510534 -1.2286028 -0.75593622 0.32736075
## P11554_217 -0.7976451 -0.38630189 -1.2468601 -0.69624509 1.36831255
## P11554_218 -1.0636705 -0.55550285 -0.9097607 -0.38368235 0.82956607
## P11554_225 0.7457063 1.03440723 1.8093692 1.65373582 -0.58792335
## P11554_226 0.7217992 2.18403381 0.9913130 2.19601391 -1.39700313
## P11554_227 1.4982480 2.13977462 1.2807324 1.14285646 0.17120883
## P11554_228 -0.2674902 -0.02083546 1.5576186 0.97744469 0.89885585
## P11554_229 -0.4311000 0.43659602 0.8619424 0.86014130 0.49114158
## P11554_230 1.9238302 1.26477682 0.8149363 -0.40103366 1.44242545
## AT2G46020 AT4G16280 AT2G24740 AT2G28290 AT1G54490
## P11554_207 -2.11482087 -1.60609279 -0.89283517 -1.598407729 -1.54786562
## P11554_208 -0.76055589 -0.64270967 -0.83954206 -0.897973326 -1.19977274
## P11554_209 -0.93105039 -0.40077172 -0.38666930 -0.729718839 -0.60761995
## P11554_210 0.63188861 0.54033742 0.82923747 -0.225498472 0.47977619
## P11554_211 0.64185366 0.02283693 1.31162567 0.009059281 0.70415571
## P11554_212 1.76806713 0.48298831 0.94706688 0.652195899 1.02374449
## P11554_213 -0.57256968 -1.50219360 -1.13824200 -1.303445640 -1.46135676
## P11554_214 -0.19431995 -1.17021464 -1.29534712 -0.739814054 -0.94449463
## P11554_215 -0.73784215 -1.67026148 -1.48696380 -1.362540984 -0.97350789
## P11554_216 1.24563735 0.07095517 -0.46405705 0.114598826 -0.19211720
## P11554_217 1.19634758 -0.22548472 -0.22244273 0.600958661 0.06983100
## P11554_218 1.07591008 -0.21030651 -0.29347854 0.324075474 0.23425133
## P11554_225 -0.66171780 0.78526880 -0.13912917 -0.064865493 -0.33571819
## P11554_226 -0.97023459 1.29736714 -0.06123914 0.108255228 0.05210359
## P11554_227 -0.27560680 1.19113593 -0.25043656 0.685340782 0.43097040
## P11554_228 -0.13964526 0.96416663 1.38409007 0.948210616 1.13749573
## P11554_229 0.01148381 0.97211127 1.57471041 1.187784646 1.08784197
## P11554_230 0.78717517 1.10086753 1.42365215 2.291785125 2.04228257
## AT3G17590 AT2G47620 AT2G35160 AT1G73100 AT5G04940
## P11554_207 -1.2468051 1.21714610 1.69552651 1.06442987 0.6317203
## P11554_208 0.8541754 1.14201626 0.80363708 1.27194929 1.4637083
## P11554_209 0.6562776 0.05301934 1.06842860 0.86260167 1.5834137
## P11554_210 -0.8398321 -0.33839501 -0.12521438 -0.33324870 -0.5006752
## P11554_211 0.5892378 -0.14389833 -0.34248896 0.31421986 -0.4920535
## P11554_212 0.4792745 0.41673316 -0.22351942 0.13791304 -0.2119378
## P11554_213 -1.1185429 1.59438415 1.15862843 1.27219821 1.1539268
## P11554_214 0.3532512 1.40114810 1.28645859 1.51063194 1.5056619
## P11554_215 1.4912575 1.36951604 1.25297147 0.18465356 1.2956360
## P11554_216 0.3019832 -0.33512076 0.02654326 -0.66067776 -0.5957262
## P11554_217 0.1260616 -0.13290120 -0.02932019 -0.39274707 -0.8052234
## P11554_218 0.6264243 -0.24335660 -0.20828993 -1.44670415 -0.9816625
## P11554_225 -1.2047506 -1.67228760 -1.11168565 -0.09829489 0.0151329
## P11554_226 -0.7553896 -0.34426659 -0.46789946 -1.34181677 -0.3701368
## P11554_227 1.1174281 -1.05473299 -0.68250224 0.25267147 -0.4950853
## P11554_228 -1.8954013 -0.98957757 -1.43170905 0.37637412 -0.6760304
## P11554_229 1.2155707 -1.44148562 -1.26794432 -1.15577508 -1.5370676
## P11554_230 -0.7502203 -0.49794089 -1.40162034 -1.81837860 -0.9836013
## AT1G77300
## P11554_207 -0.44392476
## P11554_208 0.82357031
## P11554_209 1.19297684
## P11554_210 -1.06961488
## P11554_211 0.50952611
## P11554_212 0.72323035
## P11554_213 0.58801139
## P11554_214 1.95529664
## P11554_215 1.70356728
## P11554_216 -0.77968835
## P11554_217 -0.93586954
## P11554_218 -1.10964201
## P11554_225 -0.59548791
## P11554_226 -0.58486253
## P11554_227 0.08492790
## P11554_228 0.05250601
## P11554_229 -1.20943891
## P11554_230 -0.90508394
##
## $`GO:0040029`$rowDendrogram
## 'dendrogram' with 2 branches and 16 members total, at height 1.807101
##
## $`GO:0040029`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0040029`$breaks
## [1] -2.2917851 -2.2459494 -2.2001137 -2.1542780 -2.1084423 -2.0626066
## [7] -2.0167709 -1.9709352 -1.9250995 -1.8792638 -1.8334281 -1.7875924
## [13] -1.7417567 -1.6959210 -1.6500853 -1.6042496 -1.5584139 -1.5125782
## [19] -1.4667425 -1.4209068 -1.3750711 -1.3292354 -1.2833997 -1.2375640
## [25] -1.1917283 -1.1458926 -1.1000569 -1.0542212 -1.0083855 -0.9625498
## [31] -0.9167140 -0.8708783 -0.8250426 -0.7792069 -0.7333712 -0.6875355
## [37] -0.6416998 -0.5958641 -0.5500284 -0.5041927 -0.4583570 -0.4125213
## [43] -0.3666856 -0.3208499 -0.2750142 -0.2291785 -0.1833428 -0.1375071
## [49] -0.0916714 -0.0458357 0.0000000 0.0458357 0.0916714 0.1375071
## [55] 0.1833428 0.2291785 0.2750142 0.3208499 0.3666856 0.4125213
## [61] 0.4583570 0.5041927 0.5500284 0.5958641 0.6416998 0.6875355
## [67] 0.7333712 0.7792069 0.8250426 0.8708783 0.9167140 0.9625498
## [73] 1.0083855 1.0542212 1.1000569 1.1458926 1.1917283 1.2375640
## [79] 1.2833997 1.3292354 1.3750711 1.4209068 1.4667425 1.5125782
## [85] 1.5584139 1.6042496 1.6500853 1.6959210 1.7417567 1.7875924
## [91] 1.8334281 1.8792638 1.9250995 1.9709352 2.0167709 2.0626066
## [97] 2.1084423 2.1542780 2.2001137 2.2459494 2.2917851
##
## $`GO:0040029`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0040029`$colorTable
## low high color
## 1 -2.2917851 -2.2459494 #0000FF
## 2 -2.2459494 -2.2001137 #0505FF
## 3 -2.2001137 -2.1542780 #0A0AFF
## 4 -2.1542780 -2.1084423 #0F0FFF
## 5 -2.1084423 -2.0626066 #1414FF
## 6 -2.0626066 -2.0167709 #1919FF
## 7 -2.0167709 -1.9709352 #1E1EFF
## 8 -1.9709352 -1.9250995 #2424FF
## 9 -1.9250995 -1.8792638 #2929FF
## 10 -1.8792638 -1.8334281 #2E2EFF
## 11 -1.8334281 -1.7875924 #3333FF
## 12 -1.7875924 -1.7417567 #3838FF
## 13 -1.7417567 -1.6959210 #3D3DFF
## 14 -1.6959210 -1.6500853 #4242FF
## 15 -1.6500853 -1.6042496 #4848FF
## 16 -1.6042496 -1.5584139 #4D4DFF
## 17 -1.5584139 -1.5125782 #5252FF
## 18 -1.5125782 -1.4667425 #5757FF
## 19 -1.4667425 -1.4209068 #5C5CFF
## 20 -1.4209068 -1.3750711 #6161FF
## 21 -1.3750711 -1.3292354 #6767FF
## 22 -1.3292354 -1.2833997 #6C6CFF
## 23 -1.2833997 -1.2375640 #7171FF
## 24 -1.2375640 -1.1917283 #7676FF
## 25 -1.1917283 -1.1458926 #7B7BFF
## 26 -1.1458926 -1.1000569 #8080FF
## 27 -1.1000569 -1.0542212 #8585FF
## 28 -1.0542212 -1.0083855 #8B8BFF
## 29 -1.0083855 -0.9625498 #9090FF
## 30 -0.9625498 -0.9167140 #9595FF
## 31 -0.9167140 -0.8708783 #9A9AFF
## 32 -0.8708783 -0.8250426 #9F9FFF
## 33 -0.8250426 -0.7792069 #A4A4FF
## 34 -0.7792069 -0.7333712 #AAAAFF
## 35 -0.7333712 -0.6875355 #AFAFFF
## 36 -0.6875355 -0.6416998 #B4B4FF
## 37 -0.6416998 -0.5958641 #B9B9FF
## 38 -0.5958641 -0.5500284 #BEBEFF
## 39 -0.5500284 -0.5041927 #C3C3FF
## 40 -0.5041927 -0.4583570 #C8C8FF
## 41 -0.4583570 -0.4125213 #CECEFF
## 42 -0.4125213 -0.3666856 #D3D3FF
## 43 -0.3666856 -0.3208499 #D8D8FF
## 44 -0.3208499 -0.2750142 #DDDDFF
## 45 -0.2750142 -0.2291785 #E2E2FF
## 46 -0.2291785 -0.1833428 #E7E7FF
## 47 -0.1833428 -0.1375071 #ECECFF
## 48 -0.1375071 -0.0916714 #F2F2FF
## 49 -0.0916714 -0.0458357 #F7F7FF
## 50 -0.0458357 0.0000000 #FCFCFF
## 51 0.0000000 0.0458357 #FFFCFC
## 52 0.0458357 0.0916714 #FFF7F7
## 53 0.0916714 0.1375071 #FFF2F2
## 54 0.1375071 0.1833428 #FFECEC
## 55 0.1833428 0.2291785 #FFE7E7
## 56 0.2291785 0.2750142 #FFE2E2
## 57 0.2750142 0.3208499 #FFDDDD
## 58 0.3208499 0.3666856 #FFD8D8
## 59 0.3666856 0.4125213 #FFD3D3
## 60 0.4125213 0.4583570 #FFCECE
## 61 0.4583570 0.5041927 #FFC8C8
## 62 0.5041927 0.5500284 #FFC3C3
## 63 0.5500284 0.5958641 #FFBEBE
## 64 0.5958641 0.6416998 #FFB9B9
## 65 0.6416998 0.6875355 #FFB4B4
## 66 0.6875355 0.7333712 #FFAFAF
## 67 0.7333712 0.7792069 #FFA9A9
## 68 0.7792069 0.8250426 #FFA4A4
## 69 0.8250426 0.8708783 #FF9F9F
## 70 0.8708783 0.9167140 #FF9A9A
## 71 0.9167140 0.9625498 #FF9595
## 72 0.9625498 1.0083855 #FF9090
## 73 1.0083855 1.0542212 #FF8B8B
## 74 1.0542212 1.1000569 #FF8585
## 75 1.1000569 1.1458926 #FF8080
## 76 1.1458926 1.1917283 #FF7B7B
## 77 1.1917283 1.2375640 #FF7676
## 78 1.2375640 1.2833997 #FF7171
## 79 1.2833997 1.3292354 #FF6C6C
## 80 1.3292354 1.3750711 #FF6767
## 81 1.3750711 1.4209068 #FF6161
## 82 1.4209068 1.4667425 #FF5C5C
## 83 1.4667425 1.5125782 #FF5757
## 84 1.5125782 1.5584139 #FF5252
## 85 1.5584139 1.6042496 #FF4D4D
## 86 1.6042496 1.6500853 #FF4848
## 87 1.6500853 1.6959210 #FF4242
## 88 1.6959210 1.7417567 #FF3D3D
## 89 1.7417567 1.7875924 #FF3838
## 90 1.7875924 1.8334281 #FF3333
## 91 1.8334281 1.8792638 #FF2E2E
## 92 1.8792638 1.9250995 #FF2929
## 93 1.9250995 1.9709352 #FF2424
## 94 1.9709352 2.0167709 #FF1E1E
## 95 2.0167709 2.0626066 #FF1919
## 96 2.0626066 2.1084423 #FF1414
## 97 2.1084423 2.1542780 #FF0F0F
## 98 2.1542780 2.2001137 #FF0A0A
## 99 2.2001137 2.2459494 #FF0505
## 100 2.2459494 2.2917851 #FF0000
##
## $`GO:0040029`$layout
## $`GO:0040029`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0040029`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0040029`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0048522`
## $`GO:0048522`$rowInd
## [1] 10 23 16 11 7 5 26 4 6 3 19 13 17 9 1 21 18 25 28 12 14 2 22 8 30
## [26] 24 15 20 29 27 31
##
## $`GO:0048522`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0048522`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0048522`$carpet
## AT2G19930 AT4G30870 AT3G07740 AT2G35550 AT1G69600
## P11554_207 -0.71259827 0.32341066 0.5921740 0.16650880 0.4374851
## P11554_208 -0.48033351 -0.20833965 0.0075247 0.52115990 0.3628104
## P11554_209 -0.75353207 0.68961960 -1.7724890 0.15508676 -0.2535749
## P11554_210 1.26007726 0.45888379 0.5392714 0.81336584 0.2933758
## P11554_211 0.91986333 1.00566637 0.6355243 0.20619779 0.9066505
## P11554_212 1.39488401 1.41219409 -0.9696471 1.81688163 0.5467576
## P11554_213 -1.43359813 -1.09782016 -0.2752977 0.35613935 0.5577970
## P11554_214 -1.11263353 -1.28543426 -0.1933341 -0.19152338 0.9522882
## P11554_215 -1.77615100 -0.27233609 0.2554295 1.06255028 0.8500548
## P11554_216 0.75183313 1.13801657 0.1894817 1.08006286 0.8869029
## P11554_217 0.49771482 0.70159693 0.9268221 -0.50859519 0.8151993
## P11554_218 0.63709795 0.47100616 1.2185133 0.12145410 1.0625014
## P11554_225 -1.08938225 -2.17175940 -2.1475529 -2.43892366 -1.9955856
## P11554_226 -0.60129240 -1.63930026 0.1063612 0.09327791 -1.9042801
## P11554_227 0.02380837 -0.46820861 -1.3903312 -1.69528300 -1.1857678
## P11554_228 0.89144242 0.23474326 1.5652504 -0.29103295 -0.6337296
## P11554_229 0.95127731 0.73512524 0.5212804 -0.30185295 -0.9625787
## P11554_230 0.63152257 -0.02706425 0.1910190 -0.96547409 -0.7363063
## AT1G48380 AT5G06960 AT1G32810 AT1G65660 AT1G17680 AT3G54610
## P11554_207 -0.36284931 -0.9786850 -0.8006648 -1.08605790 -1.50037743 -0.3543048
## P11554_208 -1.12235789 -1.8284987 -0.4997031 -0.79985668 -1.05420923 -0.5837267
## P11554_209 -1.21007973 0.1803435 -0.0770854 -1.11183554 -0.79964576 -0.6502996
## P11554_210 0.85884708 0.6214203 0.3305063 0.36821018 0.03158000 -0.9006017
## P11554_211 -0.28437464 0.8629420 0.7479220 0.21489739 0.44848291 -0.9124209
## P11554_212 0.55505498 1.6060395 1.0868217 0.68750255 1.08378374 -1.0233498
## P11554_213 1.80538484 -1.1450887 -1.8457665 -1.06436553 -0.97954503 -1.0373621
## P11554_214 -2.02383320 -1.0458249 -1.1883797 -1.69273997 -1.18594999 -0.1074923
## P11554_215 -1.05416379 -0.2853831 -1.7791999 -1.29473330 -1.46268172 -0.1794502
## P11554_216 0.77031768 -0.5731410 -0.8086551 -0.55404105 0.15427208 -0.5627357
## P11554_217 -0.26944463 -0.6544871 0.1798691 0.05677714 0.42286496 -0.7995589
## P11554_218 -0.69468302 -0.4506352 -0.1787959 0.08932535 -0.11581606 -0.7537306
## P11554_225 -0.05069506 2.1590705 0.4237995 0.32201626 0.23573585 1.4398608
## P11554_226 0.04645283 0.4605729 0.4442511 0.82988312 -0.01406908 1.6786159
## P11554_227 1.15712951 0.4646469 0.2513076 1.18504516 0.63592792 1.5393115
## P11554_228 0.47676491 -0.2212765 0.7683739 1.13070629 1.04133181 0.8919935
## P11554_229 1.35245991 0.5330716 1.1707198 1.10969883 0.94661438 1.0166099
## P11554_230 0.05006955 0.2949130 1.7746793 1.60956770 2.11170066 1.2986417
## AT2G41070 AT3G15180 AT1G79880 AT1G01160 AT4G16440
## P11554_207 -0.6750321 -1.1819567 1.0595925326 -0.26941664 0.9109396
## P11554_208 -0.7987184 -0.7850309 -0.5619370097 0.80531044 1.0012075
## P11554_209 -0.5743810 -0.4298338 1.0884648175 2.18384822 0.1954302
## P11554_210 -0.6525531 -0.6275433 -0.0129433584 -0.93134294 -2.2096651
## P11554_211 -0.7047453 -0.5817730 -0.2784627473 -0.54050670 -1.1421248
## P11554_212 -0.5378328 0.2136058 -0.3704435123 -0.57993826 -0.9835008
## P11554_213 -0.3633846 -0.3891552 1.2791670627 1.70284716 -0.3500896
## P11554_214 -0.6757451 -0.2931934 0.3342330708 0.35662357 0.2892436
## P11554_215 -0.8941975 -0.2495780 1.5061056444 1.38296137 1.6423301
## P11554_216 -0.4941203 -0.9931870 -2.0279736955 -0.44071513 -0.4663315
## P11554_217 -0.9097317 -0.7048529 0.0007924591 -1.27081306 -0.2039709
## P11554_218 -0.8116053 -1.0347773 -1.6750078983 -0.94780265 -0.4977975
## P11554_225 1.3666999 0.4824155 -1.0076406107 -0.59295215 -0.9868317
## P11554_226 1.5403967 0.4757334 -0.2824559079 0.30581777 0.3090278
## P11554_227 1.6668306 0.6686940 0.7470668778 0.13698932 -0.3289292
## P11554_228 1.1759165 1.3661860 -0.9378956802 -1.37515107 0.2420137
## P11554_229 1.3960676 1.7688358 0.7200185545 -0.03057578 1.2504948
## P11554_230 0.9461360 2.2954110 0.4193194009 0.10481655 1.3285538
## AT3G26744 AT5G06950 AT5G18950 AT2G39090 AT2G43190
## P11554_207 -0.1408875 -0.58117720 1.01617268 0.04021049 0.97210897
## P11554_208 1.0612286 -0.63391844 0.01265348 0.65129975 0.35211199
## P11554_209 0.8026894 1.10949397 -0.90486223 0.47299516 -0.31179285
## P11554_210 -1.8046950 0.81582399 0.35286424 -0.02958522 0.01570303
## P11554_211 -1.6023663 -1.57562954 -0.23416569 0.15997364 -1.28493011
## P11554_212 -0.3546772 -0.97746185 -1.15241560 1.63172559 0.25917568
## P11554_213 0.3725951 0.76795321 1.46229257 0.80953688 1.56491015
## P11554_214 0.9430621 0.63958559 1.52937480 0.35873548 0.84575829
## P11554_215 0.8644587 -0.12008532 -0.22429098 1.61449580 2.18816245
## P11554_216 -0.7761949 -1.65563592 0.03520998 -1.04610082 0.01013230
## P11554_217 -0.1638817 1.88170919 -0.22224424 0.07643447 -0.33982788
## P11554_218 -1.2073504 -0.62999194 0.17753089 0.02416260 0.39131527
## P11554_225 1.3339966 0.69817645 1.22026475 -0.11091680 -0.65874180
## P11554_226 0.8731958 -0.10649612 -0.86618536 -0.50489231 -1.05556847
## P11554_227 1.3588324 -0.69808066 -1.56972940 -0.24092249 -1.95764161
## P11554_228 -0.5563749 -0.06415515 1.46067770 -1.91661783 -0.37125485
## P11554_229 -0.8142173 1.46081124 -1.08970044 -2.25825599 -0.61312715
## P11554_230 -0.1894134 -0.33092148 -1.00344715 0.26772159 -0.00649341
## AT1G13050 AT4G25540 AT1G72050 AT5G24630 AT5G03070 AT2G44270
## P11554_207 1.57701290 1.3932473 1.4206022 1.0743095 1.0843934 1.077906351
## P11554_208 0.90045785 1.5735449 1.0566987 1.3757075 1.1906874 0.836079307
## P11554_209 0.03242780 1.1728616 1.0458398 1.0144499 1.1003268 1.036027308
## P11554_210 -0.55003638 -0.8270198 -0.3881547 -0.8778429 -0.7938045 -0.534053045
## P11554_211 0.08857631 -0.4053344 -0.2116180 -0.5962284 -0.9188667 -0.946511254
## P11554_212 -0.50189304 -0.5168293 -0.2893867 -0.5581953 -0.8337589 -0.848215170
## P11554_213 1.93545688 1.4722173 1.3427227 1.5267440 1.4414086 1.472527508
## P11554_214 0.30991393 1.3792874 1.5731530 1.2634081 1.4798569 1.480110794
## P11554_215 1.52640899 1.1210326 1.3154318 1.7658322 1.6814125 1.423104434
## P11554_216 -0.18087356 -0.4508706 -0.1709585 -0.6972165 -0.5110464 -0.969628804
## P11554_217 -0.68810998 -0.6349829 -0.3080097 -0.7384687 -0.9745722 -0.370489771
## P11554_218 -0.66062461 -0.7591269 -0.4256330 -0.5601200 -0.9442375 -0.004867024
## P11554_225 0.05387175 -0.8778887 -0.9731745 -0.7628212 -0.2530259 -0.177670971
## P11554_226 -1.28809708 -0.3951791 -0.7227649 -0.3008009 -0.4359663 0.487827247
## P11554_227 0.10045422 -0.8204350 -0.9784933 -0.3160694 -0.3690467 -0.415800988
## P11554_228 0.26204280 -0.8952088 -0.7798201 -0.9815029 -0.9254630 -1.389881557
## P11554_229 -1.57892418 -0.8412749 -1.2908742 -0.9380702 -0.6873088 -1.123181125
## P11554_230 -1.33806460 -0.6880407 -1.2155604 -0.6931147 -0.3309889 -1.033283240
## AT4G15090 AT5G19020 AT5G14960 AT5G27750
## P11554_207 1.42305829 1.19873909 1.30105079 1.74496611
## P11554_208 1.05015028 1.56869941 0.64930854 1.49276501
## P11554_209 0.29508402 0.90764759 0.65969805 0.81619744
## P11554_210 -0.05380457 0.01592491 1.05538722 0.33234631
## P11554_211 -0.61364529 0.97297751 0.11885258 -0.35160956
## P11554_212 -0.65438657 -0.53256415 -1.23811032 -1.12728586
## P11554_213 1.10766483 1.35410872 1.63038810 0.44496816
## P11554_214 1.76344021 1.36999215 1.06496283 1.08469022
## P11554_215 1.19614689 0.30362426 1.26759994 1.64371833
## P11554_216 -0.34400027 -0.81167040 -0.86670681 -0.88839267
## P11554_217 0.72244037 0.17180761 -0.56669447 -0.02460024
## P11554_218 -1.09154277 -0.80539316 -0.18418527 -0.80778542
## P11554_225 -0.28118019 -0.62913062 0.04420902 -0.44053546
## P11554_226 -0.50473677 -1.11781209 -1.26475683 -0.59916053
## P11554_227 -0.76194011 -0.70964462 -1.07104673 -1.24315886
## P11554_228 -0.79859079 -0.70221300 -1.28911556 -0.57433499
## P11554_229 -0.58886273 -1.30836287 -0.74066626 -1.24100204
## P11554_230 -1.86529483 -1.24673035 -0.57017481 -0.26178595
##
## $`GO:0048522`$rowDendrogram
## 'dendrogram' with 2 branches and 31 members total, at height 2.195944
##
## $`GO:0048522`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0048522`$breaks
## [1] -2.43892366 -2.39014518 -2.34136671 -2.29258824 -2.24380976 -2.19503129
## [7] -2.14625282 -2.09747435 -2.04869587 -1.99991740 -1.95113893 -1.90236045
## [13] -1.85358198 -1.80480351 -1.75602503 -1.70724656 -1.65846809 -1.60968961
## [19] -1.56091114 -1.51213267 -1.46335419 -1.41457572 -1.36579725 -1.31701878
## [25] -1.26824030 -1.21946183 -1.17068336 -1.12190488 -1.07312641 -1.02434794
## [31] -0.97556946 -0.92679099 -0.87801252 -0.82923404 -0.78045557 -0.73167710
## [37] -0.68289862 -0.63412015 -0.58534168 -0.53656320 -0.48778473 -0.43900626
## [43] -0.39022779 -0.34144931 -0.29267084 -0.24389237 -0.19511389 -0.14633542
## [49] -0.09755695 -0.04877847 0.00000000 0.04877847 0.09755695 0.14633542
## [55] 0.19511389 0.24389237 0.29267084 0.34144931 0.39022779 0.43900626
## [61] 0.48778473 0.53656320 0.58534168 0.63412015 0.68289862 0.73167710
## [67] 0.78045557 0.82923404 0.87801252 0.92679099 0.97556946 1.02434794
## [73] 1.07312641 1.12190488 1.17068336 1.21946183 1.26824030 1.31701878
## [79] 1.36579725 1.41457572 1.46335419 1.51213267 1.56091114 1.60968961
## [85] 1.65846809 1.70724656 1.75602503 1.80480351 1.85358198 1.90236045
## [91] 1.95113893 1.99991740 2.04869587 2.09747435 2.14625282 2.19503129
## [97] 2.24380976 2.29258824 2.34136671 2.39014518 2.43892366
##
## $`GO:0048522`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0048522`$colorTable
## low high color
## 1 -2.43892366 -2.39014518 #0000FF
## 2 -2.39014518 -2.34136671 #0505FF
## 3 -2.34136671 -2.29258824 #0A0AFF
## 4 -2.29258824 -2.24380976 #0F0FFF
## 5 -2.24380976 -2.19503129 #1414FF
## 6 -2.19503129 -2.14625282 #1919FF
## 7 -2.14625282 -2.09747435 #1E1EFF
## 8 -2.09747435 -2.04869587 #2424FF
## 9 -2.04869587 -1.99991740 #2929FF
## 10 -1.99991740 -1.95113893 #2E2EFF
## 11 -1.95113893 -1.90236045 #3333FF
## 12 -1.90236045 -1.85358198 #3838FF
## 13 -1.85358198 -1.80480351 #3D3DFF
## 14 -1.80480351 -1.75602503 #4242FF
## 15 -1.75602503 -1.70724656 #4848FF
## 16 -1.70724656 -1.65846809 #4D4DFF
## 17 -1.65846809 -1.60968961 #5252FF
## 18 -1.60968961 -1.56091114 #5757FF
## 19 -1.56091114 -1.51213267 #5C5CFF
## 20 -1.51213267 -1.46335419 #6161FF
## 21 -1.46335419 -1.41457572 #6767FF
## 22 -1.41457572 -1.36579725 #6C6CFF
## 23 -1.36579725 -1.31701878 #7171FF
## 24 -1.31701878 -1.26824030 #7676FF
## 25 -1.26824030 -1.21946183 #7B7BFF
## 26 -1.21946183 -1.17068336 #8080FF
## 27 -1.17068336 -1.12190488 #8585FF
## 28 -1.12190488 -1.07312641 #8B8BFF
## 29 -1.07312641 -1.02434794 #9090FF
## 30 -1.02434794 -0.97556946 #9595FF
## 31 -0.97556946 -0.92679099 #9A9AFF
## 32 -0.92679099 -0.87801252 #9F9FFF
## 33 -0.87801252 -0.82923404 #A4A4FF
## 34 -0.82923404 -0.78045557 #AAAAFF
## 35 -0.78045557 -0.73167710 #AFAFFF
## 36 -0.73167710 -0.68289862 #B4B4FF
## 37 -0.68289862 -0.63412015 #B9B9FF
## 38 -0.63412015 -0.58534168 #BEBEFF
## 39 -0.58534168 -0.53656320 #C3C3FF
## 40 -0.53656320 -0.48778473 #C8C8FF
## 41 -0.48778473 -0.43900626 #CECEFF
## 42 -0.43900626 -0.39022779 #D3D3FF
## 43 -0.39022779 -0.34144931 #D8D8FF
## 44 -0.34144931 -0.29267084 #DDDDFF
## 45 -0.29267084 -0.24389237 #E2E2FF
## 46 -0.24389237 -0.19511389 #E7E7FF
## 47 -0.19511389 -0.14633542 #ECECFF
## 48 -0.14633542 -0.09755695 #F2F2FF
## 49 -0.09755695 -0.04877847 #F7F7FF
## 50 -0.04877847 0.00000000 #FCFCFF
## 51 0.00000000 0.04877847 #FFFCFC
## 52 0.04877847 0.09755695 #FFF7F7
## 53 0.09755695 0.14633542 #FFF2F2
## 54 0.14633542 0.19511389 #FFECEC
## 55 0.19511389 0.24389237 #FFE7E7
## 56 0.24389237 0.29267084 #FFE2E2
## 57 0.29267084 0.34144931 #FFDDDD
## 58 0.34144931 0.39022779 #FFD8D8
## 59 0.39022779 0.43900626 #FFD3D3
## 60 0.43900626 0.48778473 #FFCECE
## 61 0.48778473 0.53656320 #FFC8C8
## 62 0.53656320 0.58534168 #FFC3C3
## 63 0.58534168 0.63412015 #FFBEBE
## 64 0.63412015 0.68289862 #FFB9B9
## 65 0.68289862 0.73167710 #FFB4B4
## 66 0.73167710 0.78045557 #FFAFAF
## 67 0.78045557 0.82923404 #FFA9A9
## 68 0.82923404 0.87801252 #FFA4A4
## 69 0.87801252 0.92679099 #FF9F9F
## 70 0.92679099 0.97556946 #FF9A9A
## 71 0.97556946 1.02434794 #FF9595
## 72 1.02434794 1.07312641 #FF9090
## 73 1.07312641 1.12190488 #FF8B8B
## 74 1.12190488 1.17068336 #FF8585
## 75 1.17068336 1.21946183 #FF8080
## 76 1.21946183 1.26824030 #FF7B7B
## 77 1.26824030 1.31701878 #FF7676
## 78 1.31701878 1.36579725 #FF7171
## 79 1.36579725 1.41457572 #FF6C6C
## 80 1.41457572 1.46335419 #FF6767
## 81 1.46335419 1.51213267 #FF6161
## 82 1.51213267 1.56091114 #FF5C5C
## 83 1.56091114 1.60968961 #FF5757
## 84 1.60968961 1.65846809 #FF5252
## 85 1.65846809 1.70724656 #FF4D4D
## 86 1.70724656 1.75602503 #FF4848
## 87 1.75602503 1.80480351 #FF4242
## 88 1.80480351 1.85358198 #FF3D3D
## 89 1.85358198 1.90236045 #FF3838
## 90 1.90236045 1.95113893 #FF3333
## 91 1.95113893 1.99991740 #FF2E2E
## 92 1.99991740 2.04869587 #FF2929
## 93 2.04869587 2.09747435 #FF2424
## 94 2.09747435 2.14625282 #FF1E1E
## 95 2.14625282 2.19503129 #FF1919
## 96 2.19503129 2.24380976 #FF1414
## 97 2.24380976 2.29258824 #FF0F0F
## 98 2.29258824 2.34136671 #FF0A0A
## 99 2.34136671 2.39014518 #FF0505
## 100 2.39014518 2.43892366 #FF0000
##
## $`GO:0048522`$layout
## $`GO:0048522`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0048522`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0048522`$layout$lwid
## [1] 1.5 4.0lapply(geneList, function(x){length(x)})## $`GO:0008610`
## [1] 7
##
## $`GO:0008652`
## [1] 50
##
## $`GO:0040008`
## [1] 5
##
## $`GO:0051726`
## [1] 144
##
## $`GO:0009825`
## [1] 84
##
## $`GO:0048519`
## [1] 46
##
## $`GO:0016458`
## [1] 58
##
## $`GO:0010608`
## [1] 3
##
## $`GO:0007059`
## [1] 43
##
## $`GO:0051301`
## [1] 77
##
## $`GO:0007267`
## [1] 98
##
## $`GO:0007017`
## [1] 23
##
## $`GO:0040029`
## [1] 16
##
## $`GO:0048522`
## [1] 31lapply(geneList, function(x){length(intersect(x,PiStarvLow))})## $`GO:0008610`
## [1] 1
##
## $`GO:0008652`
## [1] 7
##
## $`GO:0040008`
## [1] 0
##
## $`GO:0051726`
## [1] 94
##
## $`GO:0009825`
## [1] 19
##
## $`GO:0048519`
## [1] 13
##
## $`GO:0016458`
## [1] 44
##
## $`GO:0010608`
## [1] 0
##
## $`GO:0007059`
## [1] 19
##
## $`GO:0051301`
## [1] 27
##
## $`GO:0007267`
## [1] 19
##
## $`GO:0007017`
## [1] 9
##
## $`GO:0040029`
## [1] 1
##
## $`GO:0048522`
## [1] 6lapply(geneList, function(x){length(intersect(x,PiStarvHigh))})## $`GO:0008610`
## [1] 0
##
## $`GO:0008652`
## [1] 7
##
## $`GO:0040008`
## [1] 1
##
## $`GO:0051726`
## [1] 4
##
## $`GO:0009825`
## [1] 11
##
## $`GO:0048519`
## [1] 2
##
## $`GO:0016458`
## [1] 1
##
## $`GO:0010608`
## [1] 1
##
## $`GO:0007059`
## [1] 0
##
## $`GO:0051301`
## [1] 3
##
## $`GO:0007267`
## [1] 3
##
## $`GO:0007017`
## [1] 1
##
## $`GO:0040029`
## [1] 1
##
## $`GO:0048522`
## [1] 3lapply(geneList, function(x){
goi <- res_Pi[rownames(res_Pi) %in% x,]
volcanoPlot(goi)
goi2 <- t(scale(t(vsd_T6[rownames(res_Pi) %in% x,])))
goi2 <- na.omit(goi2)
hm <- heatmap.2(goi2,col=hpal,
Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T6],
hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))
})
## $`GO:0008610`
## $`GO:0008610`$rowInd
## [1] 6 5 7 4 3 1 2
##
## $`GO:0008610`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0008610`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0008610`$carpet
## AT3G23530 AT3G23510 AT3G54320 AT3G23470 AT2G43710 AT2G26250
## P11554_207 -0.580561 0.9656632 1.1901044 -0.315613036 -0.4636765 -0.8866897
## P11554_208 1.230705 1.1524073 1.3799930 -1.881889602 -0.5086719 -1.4315348
## P11554_209 1.403376 0.6564052 0.4652879 -0.556125726 -0.2811387 -1.1309443
## P11554_210 -0.580561 1.2335552 1.1296868 -0.626869921 -0.3402225 0.5031475
## P11554_211 -0.580561 0.2800088 0.0434840 0.183599628 -0.3512663 0.3400428
## P11554_212 -0.580561 0.4367527 0.2257048 -0.248753080 -0.2079475 -0.4081840
## P11554_213 1.291344 1.2260649 0.8889575 -0.113096342 -1.0621916 -1.3259379
## P11554_214 1.137249 -1.0482995 0.6062896 1.153112397 -0.6561333 -0.5897074
## P11554_215 -0.580561 -1.0482995 1.2179651 0.471798353 -1.0627460 -0.9193993
## P11554_216 -0.580561 1.0834797 0.0673518 -0.709432179 -0.9398894 1.1732508
## P11554_217 -0.580561 0.4161077 -0.5650026 -0.271451529 -1.1144308 1.5883458
## P11554_218 -0.580561 0.9359512 0.2461454 0.007900055 -0.7716109 1.3331808
## P11554_225 2.484620 -1.0482995 -1.4276605 0.626294980 1.2830845 -0.6790456
## P11554_226 -0.580561 -1.0482995 -1.5421456 2.239259437 1.6394191 -0.3573238
## P11554_227 -0.580561 -1.0482995 -1.0305536 -1.881889602 1.4285532 -0.1245257
## P11554_228 -0.580561 -1.0482995 -0.3064594 0.272805155 0.5715266 0.5514491
## P11554_229 -0.580561 -1.0482995 -0.9913437 0.956833548 1.5396093 1.0823843
## P11554_230 -0.580561 -1.0482995 -1.5978050 0.693517464 1.2977326 1.2814914
## AT2G38700
## P11554_207 -1.6965200
## P11554_208 -1.1350345
## P11554_209 -0.3852578
## P11554_210 0.4836060
## P11554_211 0.2823746
## P11554_212 0.7290290
## P11554_213 -1.2677703
## P11554_214 -0.6888453
## P11554_215 -0.7989239
## P11554_216 1.3006001
## P11554_217 1.1175669
## P11554_218 1.1974590
## P11554_225 0.0885533
## P11554_226 0.6985871
## P11554_227 0.5267786
## P11554_228 -1.7554589
## P11554_229 0.7953479
## P11554_230 0.5079081
##
## $`GO:0008610`$rowDendrogram
## 'dendrogram' with 2 branches and 7 members total, at height 1.153919
##
## $`GO:0008610`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0008610`$breaks
## [1] -2.48461954 -2.43492715 -2.38523476 -2.33554237 -2.28584998 -2.23615759
## [7] -2.18646520 -2.13677281 -2.08708041 -2.03738802 -1.98769563 -1.93800324
## [13] -1.88831085 -1.83861846 -1.78892607 -1.73923368 -1.68954129 -1.63984890
## [19] -1.59015651 -1.54046412 -1.49077172 -1.44107933 -1.39138694 -1.34169455
## [25] -1.29200216 -1.24230977 -1.19261738 -1.14292499 -1.09323260 -1.04354021
## [31] -0.99384782 -0.94415543 -0.89446303 -0.84477064 -0.79507825 -0.74538586
## [37] -0.69569347 -0.64600108 -0.59630869 -0.54661630 -0.49692391 -0.44723152
## [43] -0.39753913 -0.34784674 -0.29815434 -0.24846195 -0.19876956 -0.14907717
## [49] -0.09938478 -0.04969239 0.00000000 0.04969239 0.09938478 0.14907717
## [55] 0.19876956 0.24846195 0.29815434 0.34784674 0.39753913 0.44723152
## [61] 0.49692391 0.54661630 0.59630869 0.64600108 0.69569347 0.74538586
## [67] 0.79507825 0.84477064 0.89446303 0.94415543 0.99384782 1.04354021
## [73] 1.09323260 1.14292499 1.19261738 1.24230977 1.29200216 1.34169455
## [79] 1.39138694 1.44107933 1.49077172 1.54046412 1.59015651 1.63984890
## [85] 1.68954129 1.73923368 1.78892607 1.83861846 1.88831085 1.93800324
## [91] 1.98769563 2.03738802 2.08708041 2.13677281 2.18646520 2.23615759
## [97] 2.28584998 2.33554237 2.38523476 2.43492715 2.48461954
##
## $`GO:0008610`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0008610`$colorTable
## low high color
## 1 -2.48461954 -2.43492715 #0000FF
## 2 -2.43492715 -2.38523476 #0505FF
## 3 -2.38523476 -2.33554237 #0A0AFF
## 4 -2.33554237 -2.28584998 #0F0FFF
## 5 -2.28584998 -2.23615759 #1414FF
## 6 -2.23615759 -2.18646520 #1919FF
## 7 -2.18646520 -2.13677281 #1E1EFF
## 8 -2.13677281 -2.08708041 #2424FF
## 9 -2.08708041 -2.03738802 #2929FF
## 10 -2.03738802 -1.98769563 #2E2EFF
## 11 -1.98769563 -1.93800324 #3333FF
## 12 -1.93800324 -1.88831085 #3838FF
## 13 -1.88831085 -1.83861846 #3D3DFF
## 14 -1.83861846 -1.78892607 #4242FF
## 15 -1.78892607 -1.73923368 #4848FF
## 16 -1.73923368 -1.68954129 #4D4DFF
## 17 -1.68954129 -1.63984890 #5252FF
## 18 -1.63984890 -1.59015651 #5757FF
## 19 -1.59015651 -1.54046412 #5C5CFF
## 20 -1.54046412 -1.49077172 #6161FF
## 21 -1.49077172 -1.44107933 #6767FF
## 22 -1.44107933 -1.39138694 #6C6CFF
## 23 -1.39138694 -1.34169455 #7171FF
## 24 -1.34169455 -1.29200216 #7676FF
## 25 -1.29200216 -1.24230977 #7B7BFF
## 26 -1.24230977 -1.19261738 #8080FF
## 27 -1.19261738 -1.14292499 #8585FF
## 28 -1.14292499 -1.09323260 #8B8BFF
## 29 -1.09323260 -1.04354021 #9090FF
## 30 -1.04354021 -0.99384782 #9595FF
## 31 -0.99384782 -0.94415543 #9A9AFF
## 32 -0.94415543 -0.89446303 #9F9FFF
## 33 -0.89446303 -0.84477064 #A4A4FF
## 34 -0.84477064 -0.79507825 #AAAAFF
## 35 -0.79507825 -0.74538586 #AFAFFF
## 36 -0.74538586 -0.69569347 #B4B4FF
## 37 -0.69569347 -0.64600108 #B9B9FF
## 38 -0.64600108 -0.59630869 #BEBEFF
## 39 -0.59630869 -0.54661630 #C3C3FF
## 40 -0.54661630 -0.49692391 #C8C8FF
## 41 -0.49692391 -0.44723152 #CECEFF
## 42 -0.44723152 -0.39753913 #D3D3FF
## 43 -0.39753913 -0.34784674 #D8D8FF
## 44 -0.34784674 -0.29815434 #DDDDFF
## 45 -0.29815434 -0.24846195 #E2E2FF
## 46 -0.24846195 -0.19876956 #E7E7FF
## 47 -0.19876956 -0.14907717 #ECECFF
## 48 -0.14907717 -0.09938478 #F2F2FF
## 49 -0.09938478 -0.04969239 #F7F7FF
## 50 -0.04969239 0.00000000 #FCFCFF
## 51 0.00000000 0.04969239 #FFFCFC
## 52 0.04969239 0.09938478 #FFF7F7
## 53 0.09938478 0.14907717 #FFF2F2
## 54 0.14907717 0.19876956 #FFECEC
## 55 0.19876956 0.24846195 #FFE7E7
## 56 0.24846195 0.29815434 #FFE2E2
## 57 0.29815434 0.34784674 #FFDDDD
## 58 0.34784674 0.39753913 #FFD8D8
## 59 0.39753913 0.44723152 #FFD3D3
## 60 0.44723152 0.49692391 #FFCECE
## 61 0.49692391 0.54661630 #FFC8C8
## 62 0.54661630 0.59630869 #FFC3C3
## 63 0.59630869 0.64600108 #FFBEBE
## 64 0.64600108 0.69569347 #FFB9B9
## 65 0.69569347 0.74538586 #FFB4B4
## 66 0.74538586 0.79507825 #FFAFAF
## 67 0.79507825 0.84477064 #FFA9A9
## 68 0.84477064 0.89446303 #FFA4A4
## 69 0.89446303 0.94415543 #FF9F9F
## 70 0.94415543 0.99384782 #FF9A9A
## 71 0.99384782 1.04354021 #FF9595
## 72 1.04354021 1.09323260 #FF9090
## 73 1.09323260 1.14292499 #FF8B8B
## 74 1.14292499 1.19261738 #FF8585
## 75 1.19261738 1.24230977 #FF8080
## 76 1.24230977 1.29200216 #FF7B7B
## 77 1.29200216 1.34169455 #FF7676
## 78 1.34169455 1.39138694 #FF7171
## 79 1.39138694 1.44107933 #FF6C6C
## 80 1.44107933 1.49077172 #FF6767
## 81 1.49077172 1.54046412 #FF6161
## 82 1.54046412 1.59015651 #FF5C5C
## 83 1.59015651 1.63984890 #FF5757
## 84 1.63984890 1.68954129 #FF5252
## 85 1.68954129 1.73923368 #FF4D4D
## 86 1.73923368 1.78892607 #FF4848
## 87 1.78892607 1.83861846 #FF4242
## 88 1.83861846 1.88831085 #FF3D3D
## 89 1.88831085 1.93800324 #FF3838
## 90 1.93800324 1.98769563 #FF3333
## 91 1.98769563 2.03738802 #FF2E2E
## 92 2.03738802 2.08708041 #FF2929
## 93 2.08708041 2.13677281 #FF2424
## 94 2.13677281 2.18646520 #FF1E1E
## 95 2.18646520 2.23615759 #FF1919
## 96 2.23615759 2.28584998 #FF1414
## 97 2.28584998 2.33554237 #FF0F0F
## 98 2.33554237 2.38523476 #FF0A0A
## 99 2.38523476 2.43492715 #FF0505
## 100 2.43492715 2.48461954 #FF0000
##
## $`GO:0008610`$layout
## $`GO:0008610`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0008610`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0008610`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0008652`
## $`GO:0008652`$rowInd
## [1] 7 25 6 47 12 13 3 8 43 28 18 39 21 1 44 23 34 49 10 16 46 9 38 30 15
## [26] 11 45 20 35 4 19 29 31 41 24 5 36 48 33 32 2 40 37 42 14 22 27 26 17
##
## $`GO:0008652`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0008652`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0008652`$carpet
## AT1G74960 AT3G25860 AT1G70310 AT5G61130 AT2G21330
## P11554_207 0.69680077 0.65070346 0.71737202 0.54006245 0.50846136
## P11554_208 1.11361739 1.03823571 1.02807959 0.57802113 0.88971593
## P11554_209 0.50847843 0.68539537 1.54779155 0.66827943 1.63257010
## P11554_210 -1.05691438 -0.94527232 -0.08393869 -0.37181561 0.01063041
## P11554_211 -0.80783948 -0.31718330 -0.48871238 -0.49997556 0.39941787
## P11554_212 -0.66059767 0.20921555 -0.22559678 -0.76360426 0.36201018
## P11554_213 1.49305345 1.39491023 1.28152254 1.55232444 0.53192184
## P11554_214 1.43510677 1.38280805 1.11851247 1.64141825 0.87622094
## P11554_215 1.52882834 1.52893211 1.74363710 2.03470130 0.60453128
## P11554_216 -0.45377065 0.17984916 -0.37204034 0.08318727 0.61496769
## P11554_217 -0.64250596 -0.01821190 -0.09766538 0.09955149 0.50330516
## P11554_218 0.06799104 -0.22423953 0.02691345 0.05913967 0.68928641
## P11554_225 -1.03894297 -0.72400014 -1.37434189 -0.71916572 -1.19950164
## P11554_226 0.72874505 -0.03461094 -1.12618589 -0.81677969 -1.11066898
## P11554_227 0.38472863 -0.28315894 -1.02774731 -0.60537081 -0.96557786
## P11554_228 -1.43255505 -1.94106027 -1.07725420 -1.22977063 -1.82599859
## P11554_229 -0.85482935 -1.24112973 -0.70792941 -0.90468698 -0.84013972
## P11554_230 -1.00939437 -1.34118259 -0.88241644 -1.34551616 -1.68115238
## AT2G22330 AT1G11870 AT2G02500 AT5G13280 AT3G62030 AT2G37250
## P11554_207 0.3600030 1.40601935 1.1323139 0.97493471 0.9749867 0.7879539
## P11554_208 0.5818213 0.78427808 1.0416064 1.07558454 1.4939521 0.6786573
## P11554_209 0.5386437 1.43903487 1.1785170 1.06698378 1.4701032 0.7142714
## P11554_210 -1.1143749 -0.95771765 -0.8535415 -0.90307178 -0.4759532 -1.0854617
## P11554_211 -0.8906497 -0.76268302 -0.7676931 -0.92374666 -0.4829757 -1.3333650
## P11554_212 -0.8971723 -0.97085346 -0.5656003 -1.00335791 -0.6848754 -1.1980971
## P11554_213 1.4354207 1.16418585 0.9882174 1.48204626 0.9636385 1.4215207
## P11554_214 1.2830436 1.31872352 1.4880468 1.41953505 1.3198069 1.3304527
## P11554_215 0.9594543 1.10955459 1.8283809 1.59689792 1.6586409 1.5320460
## P11554_216 0.9697285 -1.36274671 -0.9448187 -0.72418759 -0.6029954 -1.0715356
## P11554_217 0.8131284 -0.26408731 -1.2103924 -0.72824365 -0.3140318 -1.1255299
## P11554_218 1.0316569 -0.76602811 -0.7323867 -0.88970090 -0.5578570 -0.9564210
## P11554_225 -1.0463746 -0.01533128 -0.6916669 -0.05968623 -0.6637228 0.4910710
## P11554_226 -1.6371387 0.49589622 -0.3018784 0.07392075 -0.2707769 0.6030424
## P11554_227 -1.4105369 -0.07670779 0.4206978 0.21745356 -0.4627143 0.5504086
## P11554_228 -0.2280579 -0.94337335 -0.8941547 -0.96108622 -1.1317419 -0.4761506
## P11554_229 -0.2976821 -1.36370140 -0.6282014 -0.75407431 -1.2380530 -0.2858994
## P11554_230 -0.4509133 -0.23446242 -0.4874459 -0.96020133 -0.9954311 -0.5769639
## AT4G34980 AT3G04790 AT1G04640 AT5G21060 AT3G10030 AT4G23600
## P11554_207 1.2181334 1.6777420 0.90786835 -0.1594711 -0.71425888 -0.4343297
## P11554_208 1.1930584 1.3714635 0.23339080 -0.5665495 0.85903837 -0.4343297
## P11554_209 1.7034661 1.2125191 1.22235861 -0.2610359 0.23105365 -0.4343297
## P11554_210 -0.4201094 -0.1253824 -1.87370847 -1.0812718 -0.90589716 -0.4343297
## P11554_211 -0.4457936 0.3022390 -1.30008954 -1.0660961 -1.09876032 -0.4343297
## P11554_212 -0.1661040 -0.5237954 -0.99067467 -0.9080492 0.01569525 -0.4343297
## P11554_213 0.8371157 0.8382797 0.65100201 0.5270152 0.95100533 -0.4343297
## P11554_214 0.6260566 1.7259446 0.09067948 -0.2155024 0.39489053 -0.4343297
## P11554_215 -0.3032921 0.5511589 0.62807426 0.6874499 -0.44056126 -0.4343297
## P11554_216 -0.7282259 -0.6387814 -0.81861174 -1.1821384 0.80707995 2.2348060
## P11554_217 -0.9509326 -0.7401881 -0.33703149 0.5911991 0.07524211 -0.4343297
## P11554_218 -1.0715469 -0.6211192 -0.31326534 -0.1657748 0.92538018 2.0500497
## P11554_225 0.6750200 -0.4411076 -1.19462127 1.3608780 1.10472088 -0.4343297
## P11554_226 0.7894891 -0.3382698 0.66969827 1.8679844 0.68451943 -0.4343297
## P11554_227 0.9230606 -0.6997736 1.19099921 1.8942168 1.37849539 2.2300905
## P11554_228 -1.1919215 -0.9099134 -0.98088372 -1.3299344 -1.57981945 -0.4343297
## P11554_229 -1.1738312 -1.2448690 0.99034915 -0.3012573 -2.12020655 -0.4343297
## P11554_230 -1.5136429 -1.3961471 1.22446611 0.3083378 -0.56761745 -0.4343297
## ATCG01070 AT2G20610 AT2G30870 AT5G60600 AT2G18950
## P11554_207 -0.7623640 -0.64076574 -1.075556853 -1.0764900 -0.64529778
## P11554_208 1.1657208 -0.54321057 -1.040397812 -0.7124701 -0.65250686
## P11554_209 -0.7623640 -0.49484692 -1.031316474 -0.4792496 -0.81434456
## P11554_210 -0.7623640 -0.13193129 -0.154565824 0.5881398 0.83118204
## P11554_211 -0.7623640 0.08570855 -0.247429788 0.3674721 0.45101957
## P11554_212 1.0774095 -0.10965085 -0.321037310 0.4553470 0.51610491
## P11554_213 -0.7623640 -1.09654604 -1.285499358 -1.9371438 -1.54646969
## P11554_214 1.0662372 -1.51825967 -1.149442952 -1.2479480 -1.42113118
## P11554_215 1.1129940 -2.08007776 -1.055372176 -2.0124164 -1.70604107
## P11554_216 -0.7623640 0.09473628 -0.015913955 0.3133818 -0.23647511
## P11554_217 -0.7623640 -0.04128825 -0.079282933 0.3178745 -0.04596798
## P11554_218 -0.7623640 -0.02777732 0.001325816 0.1943313 -0.14380873
## P11554_225 -0.7623640 0.55184100 1.011141714 0.9435786 0.44989776
## P11554_226 1.1353535 0.85113374 1.191916527 0.7738874 0.22368420
## P11554_227 1.8739498 0.75234543 1.118986319 0.7042711 0.29338218
## P11554_228 0.9543392 1.08977166 1.269369405 0.6238547 1.50815327
## P11554_229 -0.7623640 1.82236350 1.361618355 0.9179960 1.43211942
## P11554_230 -0.7623640 1.43645424 1.501457299 1.2655838 1.50649959
## AT4G33010 AT4G01900 AT2G27680 AT2G20860 AT5G42650
## P11554_207 -0.79751282 -1.13582978 -1.05348527 -1.2598737 -0.3248354
## P11554_208 -0.55673970 -0.89764884 -0.63893035 -1.4318249 -0.6562852
## P11554_209 -0.34023730 -1.09826156 -0.51812593 -0.5217087 -0.7652403
## P11554_210 0.63425542 0.38616160 0.97246226 0.6263184 1.3546674
## P11554_211 0.71857495 -0.04912305 0.23733509 0.4104294 1.2419813
## P11554_212 0.68320564 1.71141326 0.83558819 0.5004638 0.8012580
## P11554_213 -1.77797330 -1.33013075 -1.48396686 -0.8247876 -1.2747600
## P11554_214 -1.81969947 -1.37117729 -2.05906045 -1.3473488 -1.7616964
## P11554_215 -1.65581505 -1.32081032 -1.60251349 -1.7940327 -1.8022336
## P11554_216 -0.11953527 1.12370511 0.79175386 0.5527037 0.6024822
## P11554_217 -0.07237331 -0.27537111 0.03827616 -0.1222958 0.2625571
## P11554_218 -0.05646012 0.21069897 0.84596420 0.6417128 -0.1150398
## P11554_225 0.36514936 0.38214859 0.75119657 -0.1333130 0.5615251
## P11554_226 0.64998928 0.81455083 0.63715924 0.6122372 -0.2056755
## P11554_227 0.60285327 0.10235144 0.69247777 0.4552230 -0.3550316
## P11554_228 0.91733261 0.55308314 -0.20656444 0.6281641 1.5623037
## P11554_229 1.07808572 0.70509514 1.12240121 1.9005520 0.6922793
## P11554_230 1.54690007 1.48914463 0.63803226 1.1073808 0.1817440
## AT2G43750 AT4G30950 AT1G23740 AT2G43710 AT4G01050
## P11554_207 -1.04583775 0.003993676 -0.22584667 -0.4636765 -0.7528272
## P11554_208 -0.81505103 -0.198306546 -0.55302264 -0.5086719 -0.1255583
## P11554_209 -0.23704660 -0.077647458 -0.00216094 -0.2811387 0.2480305
## P11554_210 0.95950712 -0.912223420 0.69169184 -0.3402225 -0.4768122
## P11554_211 0.95652509 -0.876306994 -0.50878261 -0.3512663 -0.2537767
## P11554_212 1.66701094 -0.784227550 -0.39271632 -0.2079475 -0.2810845
## P11554_213 -1.62473798 -0.496312645 -1.33800064 -1.0621916 -1.3255333
## P11554_214 -1.30348568 -0.449952774 -1.35886878 -0.6561333 -1.1663286
## P11554_215 -1.62871998 -0.607986464 -1.36312418 -1.0627460 -1.4380530
## P11554_216 0.54483165 -1.052171022 -0.79588454 -0.9398894 -0.7259700
## P11554_217 0.36099767 -0.984969278 -0.87756101 -1.1144308 -0.6005254
## P11554_218 -0.03382125 -1.172971832 -0.38490285 -0.7716109 -0.4018680
## P11554_225 -0.49920678 1.583599296 1.50824081 1.2830845 1.3464571
## P11554_226 0.18939811 1.610741204 1.29409450 1.6394191 1.5615625
## P11554_227 -0.19240917 1.688899156 1.20014628 1.4285532 1.6975123
## P11554_228 0.53636255 0.799030603 1.23627606 0.5715266 0.5368156
## P11554_229 1.39624687 0.866912544 1.07235791 1.5396093 1.0549943
## P11554_230 0.76943623 1.059899504 0.79806379 1.2977326 1.1029648
## AT4G02680 AT4G39030 AT3G14110 AT1G68530 AT4G31500
## P11554_207 -1.3308708 -0.89323649 -0.6774154 -1.2773911296 -0.27559324
## P11554_208 -0.6491262 -1.32260405 -1.7286164 -1.1411272076 -0.97343011
## P11554_209 -0.4068994 -1.46265968 -1.4273470 -1.2175560391 -0.85951058
## P11554_210 -0.5736486 1.07827390 0.7073673 -0.2245136358 0.06207055
## P11554_211 0.3698936 0.75118372 0.2925928 -0.0008749247 0.05343234
## P11554_212 0.2498876 0.72985866 0.5915166 -0.0421397731 -0.27771953
## P11554_213 0.6474680 -0.52720613 0.9723533 -1.0223561293 -0.71752109
## P11554_214 0.3597557 -0.58190710 -0.1317693 -1.3009825678 -0.61225557
## P11554_215 1.1507537 -0.25206680 -0.4088195 -0.3481235187 -1.43547746
## P11554_216 1.0755470 1.61262712 1.0319928 1.0051780263 1.64053446
## P11554_217 2.0377186 1.50984047 0.9025211 0.8429466639 1.55301332
## P11554_218 0.8150792 1.45254155 1.5144154 0.8449938383 1.66466478
## P11554_225 -0.2395097 -0.78147541 -1.7858228 0.0059472215 -0.86797408
## P11554_226 -1.6982802 -0.85093363 -0.7230147 -0.3915162970 -0.73266993
## P11554_227 -1.6565144 -0.93370846 -0.2459403 -0.2131078070 -0.84922889
## P11554_228 -0.3695215 0.07697024 -0.4478915 1.7929434057 0.81266527
## P11554_229 -0.3498109 0.41326435 0.9831420 1.0179811837 0.97952584
## P11554_230 0.5680783 -0.01876226 0.5807355 1.6696986903 0.83547395
## AT5G62790 AT4G15560 AT4G04640 AT1G08550 AT4G38970
## P11554_207 -0.6341806 -0.5372412 0.87712894 -0.51005235 1.20992394
## P11554_208 -0.8956040 -0.2954352 0.50089512 0.09685860 0.39390680
## P11554_209 -0.8134503 -0.1309909 0.87571583 1.04007710 1.59567827
## P11554_210 0.9513698 0.7360750 0.08284325 -0.35482782 0.27481832
## P11554_211 0.7890277 0.8167837 1.10169814 1.46356155 1.19877665
## P11554_212 0.9388398 0.8128913 0.08041826 0.10030770 1.17591094
## P11554_213 -1.2865187 -1.8189039 -2.42759508 -2.34087516 -1.26141345
## P11554_214 -1.3363753 -1.8318845 -0.92414557 -0.11372175 -1.88615270
## P11554_215 -1.3204754 -1.0332935 -1.37321461 -1.86848018 -1.65299774
## P11554_216 0.7379067 1.1122793 0.34788113 -0.82836153 -0.07472965
## P11554_217 1.0654858 0.7927959 1.01573131 1.28428810 0.20605233
## P11554_218 1.4072824 1.5203153 1.76340808 0.50939019 -0.74251855
## P11554_225 -0.4972821 -0.6841027 -0.19076523 0.14701284 0.55307613
## P11554_226 -0.6914302 -0.4213188 -0.40188394 -0.47878028 -0.27887884
## P11554_227 -0.7776355 -0.6696989 -0.65886381 0.27839133 0.40243956
## P11554_228 0.1241927 -0.1996072 -0.67180641 1.11103580 -0.91255397
## P11554_229 1.2383740 1.0092049 0.06107027 -0.01423311 0.07284534
## P11554_230 1.0004733 0.8221313 -0.05851570 0.47840897 -0.27418336
## AT4G32980 AT5G09660 AT2G22990 AT3G04940 AT3G59060
## P11554_207 0.92004112 0.14099361 0.45580762 0.07594759 0.65245528
## P11554_208 0.12241376 0.52146515 1.48086563 0.70208586 1.10553240
## P11554_209 0.25246247 -0.02992938 1.00095585 0.08069749 1.76662647
## P11554_210 0.17272932 1.40067556 0.86015568 0.84365442 -0.49689535
## P11554_211 -1.24175669 0.97407161 0.61015030 0.70335111 -0.18689407
## P11554_212 -1.24175669 0.36814729 1.28177553 1.19272393 -0.38392141
## P11554_213 -1.24175669 -0.93239626 -0.22699956 -0.83527856 0.08510004
## P11554_214 1.34490530 -0.46643123 0.50806124 0.24122219 -1.05542925
## P11554_215 0.63448352 -0.34567168 -0.82860728 -0.88003542 -1.44127630
## P11554_216 0.07967647 0.45225300 0.60233570 0.92018863 0.21464713
## P11554_217 1.62712588 0.49740097 -0.09880529 0.89758721 1.37658954
## P11554_218 -0.01179248 1.47996101 1.08356161 1.45869939 1.42560635
## P11554_225 -1.24175669 -2.13488353 -1.45449941 -1.44990118 -1.84800145
## P11554_226 -1.24175669 -0.16070651 -1.23648952 -1.87342632 -0.51559588
## P11554_227 -1.24175669 -0.50242660 -1.48074015 -1.18385563 0.38725782
## P11554_228 0.47578814 -2.14102712 -1.24508912 -0.82869772 -0.28334116
## P11554_229 1.02138078 0.49650433 -0.49687459 -0.68550947 0.04422181
## P11554_230 0.81132589 0.38199979 -0.81556423 0.62054647 -0.84668194
## AT3G26900 AT2G35500
## P11554_207 0.54377085 -1.98778073
## P11554_208 1.17612531 1.33998972
## P11554_209 1.26586722 0.86188361
## P11554_210 1.66060792 0.43831689
## P11554_211 0.04427991 0.23046142
## P11554_212 0.17265105 0.50794480
## P11554_213 -0.18967186 -0.49588934
## P11554_214 -1.68374217 -0.74010512
## P11554_215 0.57390569 -0.97476811
## P11554_216 -0.97983882 -0.58030181
## P11554_217 1.35404666 0.59494191
## P11554_218 -0.84852306 0.05209774
## P11554_225 -1.19615291 -0.15017546
## P11554_226 -1.21844001 -0.52518758
## P11554_227 0.61693795 0.09284449
## P11554_228 -0.65097687 -1.42466087
## P11554_229 -0.70139765 2.22378459
## P11554_230 0.06055078 0.53660384
##
## $`GO:0008652`$rowDendrogram
## 'dendrogram' with 2 branches and 49 members total, at height 2.847438
##
## $`GO:0008652`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0008652`$breaks
## [1] -2.4275951 -2.3790432 -2.3304913 -2.2819394 -2.2333875 -2.1848356
## [7] -2.1362837 -2.0877318 -2.0391799 -1.9906280 -1.9420761 -1.8935242
## [13] -1.8449723 -1.7964204 -1.7478685 -1.6993166 -1.6507647 -1.6022128
## [19] -1.5536608 -1.5051089 -1.4565570 -1.4080051 -1.3594532 -1.3109013
## [25] -1.2623494 -1.2137975 -1.1652456 -1.1166937 -1.0681418 -1.0195899
## [31] -0.9710380 -0.9224861 -0.8739342 -0.8253823 -0.7768304 -0.7282785
## [37] -0.6797266 -0.6311747 -0.5826228 -0.5340709 -0.4855190 -0.4369671
## [43] -0.3884152 -0.3398633 -0.2913114 -0.2427595 -0.1942076 -0.1456557
## [49] -0.0971038 -0.0485519 0.0000000 0.0485519 0.0971038 0.1456557
## [55] 0.1942076 0.2427595 0.2913114 0.3398633 0.3884152 0.4369671
## [61] 0.4855190 0.5340709 0.5826228 0.6311747 0.6797266 0.7282785
## [67] 0.7768304 0.8253823 0.8739342 0.9224861 0.9710380 1.0195899
## [73] 1.0681418 1.1166937 1.1652456 1.2137975 1.2623494 1.3109013
## [79] 1.3594532 1.4080051 1.4565570 1.5051089 1.5536608 1.6022128
## [85] 1.6507647 1.6993166 1.7478685 1.7964204 1.8449723 1.8935242
## [91] 1.9420761 1.9906280 2.0391799 2.0877318 2.1362837 2.1848356
## [97] 2.2333875 2.2819394 2.3304913 2.3790432 2.4275951
##
## $`GO:0008652`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0008652`$colorTable
## low high color
## 1 -2.4275951 -2.3790432 #0000FF
## 2 -2.3790432 -2.3304913 #0505FF
## 3 -2.3304913 -2.2819394 #0A0AFF
## 4 -2.2819394 -2.2333875 #0F0FFF
## 5 -2.2333875 -2.1848356 #1414FF
## 6 -2.1848356 -2.1362837 #1919FF
## 7 -2.1362837 -2.0877318 #1E1EFF
## 8 -2.0877318 -2.0391799 #2424FF
## 9 -2.0391799 -1.9906280 #2929FF
## 10 -1.9906280 -1.9420761 #2E2EFF
## 11 -1.9420761 -1.8935242 #3333FF
## 12 -1.8935242 -1.8449723 #3838FF
## 13 -1.8449723 -1.7964204 #3D3DFF
## 14 -1.7964204 -1.7478685 #4242FF
## 15 -1.7478685 -1.6993166 #4848FF
## 16 -1.6993166 -1.6507647 #4D4DFF
## 17 -1.6507647 -1.6022128 #5252FF
## 18 -1.6022128 -1.5536608 #5757FF
## 19 -1.5536608 -1.5051089 #5C5CFF
## 20 -1.5051089 -1.4565570 #6161FF
## 21 -1.4565570 -1.4080051 #6767FF
## 22 -1.4080051 -1.3594532 #6C6CFF
## 23 -1.3594532 -1.3109013 #7171FF
## 24 -1.3109013 -1.2623494 #7676FF
## 25 -1.2623494 -1.2137975 #7B7BFF
## 26 -1.2137975 -1.1652456 #8080FF
## 27 -1.1652456 -1.1166937 #8585FF
## 28 -1.1166937 -1.0681418 #8B8BFF
## 29 -1.0681418 -1.0195899 #9090FF
## 30 -1.0195899 -0.9710380 #9595FF
## 31 -0.9710380 -0.9224861 #9A9AFF
## 32 -0.9224861 -0.8739342 #9F9FFF
## 33 -0.8739342 -0.8253823 #A4A4FF
## 34 -0.8253823 -0.7768304 #AAAAFF
## 35 -0.7768304 -0.7282785 #AFAFFF
## 36 -0.7282785 -0.6797266 #B4B4FF
## 37 -0.6797266 -0.6311747 #B9B9FF
## 38 -0.6311747 -0.5826228 #BEBEFF
## 39 -0.5826228 -0.5340709 #C3C3FF
## 40 -0.5340709 -0.4855190 #C8C8FF
## 41 -0.4855190 -0.4369671 #CECEFF
## 42 -0.4369671 -0.3884152 #D3D3FF
## 43 -0.3884152 -0.3398633 #D8D8FF
## 44 -0.3398633 -0.2913114 #DDDDFF
## 45 -0.2913114 -0.2427595 #E2E2FF
## 46 -0.2427595 -0.1942076 #E7E7FF
## 47 -0.1942076 -0.1456557 #ECECFF
## 48 -0.1456557 -0.0971038 #F2F2FF
## 49 -0.0971038 -0.0485519 #F7F7FF
## 50 -0.0485519 0.0000000 #FCFCFF
## 51 0.0000000 0.0485519 #FFFCFC
## 52 0.0485519 0.0971038 #FFF7F7
## 53 0.0971038 0.1456557 #FFF2F2
## 54 0.1456557 0.1942076 #FFECEC
## 55 0.1942076 0.2427595 #FFE7E7
## 56 0.2427595 0.2913114 #FFE2E2
## 57 0.2913114 0.3398633 #FFDDDD
## 58 0.3398633 0.3884152 #FFD8D8
## 59 0.3884152 0.4369671 #FFD3D3
## 60 0.4369671 0.4855190 #FFCECE
## 61 0.4855190 0.5340709 #FFC8C8
## 62 0.5340709 0.5826228 #FFC3C3
## 63 0.5826228 0.6311747 #FFBEBE
## 64 0.6311747 0.6797266 #FFB9B9
## 65 0.6797266 0.7282785 #FFB4B4
## 66 0.7282785 0.7768304 #FFAFAF
## 67 0.7768304 0.8253823 #FFA9A9
## 68 0.8253823 0.8739342 #FFA4A4
## 69 0.8739342 0.9224861 #FF9F9F
## 70 0.9224861 0.9710380 #FF9A9A
## 71 0.9710380 1.0195899 #FF9595
## 72 1.0195899 1.0681418 #FF9090
## 73 1.0681418 1.1166937 #FF8B8B
## 74 1.1166937 1.1652456 #FF8585
## 75 1.1652456 1.2137975 #FF8080
## 76 1.2137975 1.2623494 #FF7B7B
## 77 1.2623494 1.3109013 #FF7676
## 78 1.3109013 1.3594532 #FF7171
## 79 1.3594532 1.4080051 #FF6C6C
## 80 1.4080051 1.4565570 #FF6767
## 81 1.4565570 1.5051089 #FF6161
## 82 1.5051089 1.5536608 #FF5C5C
## 83 1.5536608 1.6022128 #FF5757
## 84 1.6022128 1.6507647 #FF5252
## 85 1.6507647 1.6993166 #FF4D4D
## 86 1.6993166 1.7478685 #FF4848
## 87 1.7478685 1.7964204 #FF4242
## 88 1.7964204 1.8449723 #FF3D3D
## 89 1.8449723 1.8935242 #FF3838
## 90 1.8935242 1.9420761 #FF3333
## 91 1.9420761 1.9906280 #FF2E2E
## 92 1.9906280 2.0391799 #FF2929
## 93 2.0391799 2.0877318 #FF2424
## 94 2.0877318 2.1362837 #FF1E1E
## 95 2.1362837 2.1848356 #FF1919
## 96 2.1848356 2.2333875 #FF1414
## 97 2.2333875 2.2819394 #FF0F0F
## 98 2.2819394 2.3304913 #FF0A0A
## 99 2.3304913 2.3790432 #FF0505
## 100 2.3790432 2.4275951 #FF0000
##
## $`GO:0008652`$layout
## $`GO:0008652`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0008652`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0008652`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0040008`
## $`GO:0040008`$rowInd
## [1] 1 2 4 3 5
##
## $`GO:0040008`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0040008`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0040008`$carpet
## AT1G16060 AT1G65380 AT5G20730 AT3G23050 AT5G60410
## P11554_207 0.003822716 0.1286015 -1.23251527 -0.6671507 -1.7224402
## P11554_208 -0.681791439 -0.6044078 -0.91320308 -0.4122325 -1.3380981
## P11554_209 -0.872819982 -0.8055421 -0.86931678 -0.5860213 -0.4263909
## P11554_210 0.273053955 0.3917698 0.81532453 0.5106285 0.3838773
## P11554_211 0.429203908 -0.4977982 0.72896261 0.6011115 -0.2377363
## P11554_212 0.681451374 -0.3305242 1.02846490 1.1684395 0.2671240
## P11554_213 1.096372826 -0.6027961 -1.57035566 -1.5226191 -1.0146178
## P11554_214 0.095011915 -0.8652510 -1.39699704 -1.0109060 -1.0815673
## P11554_215 0.200507596 -1.2925528 -1.70675448 -2.0454680 -0.3549440
## P11554_216 1.129851382 -0.7114102 0.43880780 -0.6420635 -0.7733691
## P11554_217 1.614525061 -1.1084503 0.59753997 -0.4475978 0.5214622
## P11554_218 0.467708173 -0.9836600 0.48625911 -0.4689222 -0.3605248
## P11554_225 0.184327505 1.4623565 0.01106885 0.4232849 0.1017572
## P11554_226 -1.949556256 1.5550114 0.11474269 0.6429209 0.4062798
## P11554_227 0.373249598 1.4998173 0.37750056 1.0390648 0.9106027
## P11554_228 0.167040071 1.4283198 0.93845786 0.9715217 1.5149320
## P11554_229 -2.123960003 0.3258997 0.78565164 1.4351375 1.4812144
## P11554_230 -1.087998399 1.0106167 1.36636178 1.0108719 1.7224388
##
## $`GO:0040008`$rowDendrogram
## 'dendrogram' with 2 branches and 5 members total, at height 0.810927
##
## $`GO:0040008`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0040008`$breaks
## [1] -2.1239600 -2.0814808 -2.0390016 -1.9965224 -1.9540432 -1.9115640
## [7] -1.8690848 -1.8266056 -1.7841264 -1.7416472 -1.6991680 -1.6566888
## [13] -1.6142096 -1.5717304 -1.5292512 -1.4867720 -1.4442928 -1.4018136
## [19] -1.3593344 -1.3168552 -1.2743760 -1.2318968 -1.1894176 -1.1469384
## [25] -1.1044592 -1.0619800 -1.0195008 -0.9770216 -0.9345424 -0.8920632
## [31] -0.8495840 -0.8071048 -0.7646256 -0.7221464 -0.6796672 -0.6371880
## [37] -0.5947088 -0.5522296 -0.5097504 -0.4672712 -0.4247920 -0.3823128
## [43] -0.3398336 -0.2973544 -0.2548752 -0.2123960 -0.1699168 -0.1274376
## [49] -0.0849584 -0.0424792 0.0000000 0.0424792 0.0849584 0.1274376
## [55] 0.1699168 0.2123960 0.2548752 0.2973544 0.3398336 0.3823128
## [61] 0.4247920 0.4672712 0.5097504 0.5522296 0.5947088 0.6371880
## [67] 0.6796672 0.7221464 0.7646256 0.8071048 0.8495840 0.8920632
## [73] 0.9345424 0.9770216 1.0195008 1.0619800 1.1044592 1.1469384
## [79] 1.1894176 1.2318968 1.2743760 1.3168552 1.3593344 1.4018136
## [85] 1.4442928 1.4867720 1.5292512 1.5717304 1.6142096 1.6566888
## [91] 1.6991680 1.7416472 1.7841264 1.8266056 1.8690848 1.9115640
## [97] 1.9540432 1.9965224 2.0390016 2.0814808 2.1239600
##
## $`GO:0040008`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0040008`$colorTable
## low high color
## 1 -2.1239600 -2.0814808 #0000FF
## 2 -2.0814808 -2.0390016 #0505FF
## 3 -2.0390016 -1.9965224 #0A0AFF
## 4 -1.9965224 -1.9540432 #0F0FFF
## 5 -1.9540432 -1.9115640 #1414FF
## 6 -1.9115640 -1.8690848 #1919FF
## 7 -1.8690848 -1.8266056 #1E1EFF
## 8 -1.8266056 -1.7841264 #2424FF
## 9 -1.7841264 -1.7416472 #2929FF
## 10 -1.7416472 -1.6991680 #2E2EFF
## 11 -1.6991680 -1.6566888 #3333FF
## 12 -1.6566888 -1.6142096 #3838FF
## 13 -1.6142096 -1.5717304 #3D3DFF
## 14 -1.5717304 -1.5292512 #4242FF
## 15 -1.5292512 -1.4867720 #4848FF
## 16 -1.4867720 -1.4442928 #4D4DFF
## 17 -1.4442928 -1.4018136 #5252FF
## 18 -1.4018136 -1.3593344 #5757FF
## 19 -1.3593344 -1.3168552 #5C5CFF
## 20 -1.3168552 -1.2743760 #6161FF
## 21 -1.2743760 -1.2318968 #6767FF
## 22 -1.2318968 -1.1894176 #6C6CFF
## 23 -1.1894176 -1.1469384 #7171FF
## 24 -1.1469384 -1.1044592 #7676FF
## 25 -1.1044592 -1.0619800 #7B7BFF
## 26 -1.0619800 -1.0195008 #8080FF
## 27 -1.0195008 -0.9770216 #8585FF
## 28 -0.9770216 -0.9345424 #8B8BFF
## 29 -0.9345424 -0.8920632 #9090FF
## 30 -0.8920632 -0.8495840 #9595FF
## 31 -0.8495840 -0.8071048 #9A9AFF
## 32 -0.8071048 -0.7646256 #9F9FFF
## 33 -0.7646256 -0.7221464 #A4A4FF
## 34 -0.7221464 -0.6796672 #AAAAFF
## 35 -0.6796672 -0.6371880 #AFAFFF
## 36 -0.6371880 -0.5947088 #B4B4FF
## 37 -0.5947088 -0.5522296 #B9B9FF
## 38 -0.5522296 -0.5097504 #BEBEFF
## 39 -0.5097504 -0.4672712 #C3C3FF
## 40 -0.4672712 -0.4247920 #C8C8FF
## 41 -0.4247920 -0.3823128 #CECEFF
## 42 -0.3823128 -0.3398336 #D3D3FF
## 43 -0.3398336 -0.2973544 #D8D8FF
## 44 -0.2973544 -0.2548752 #DDDDFF
## 45 -0.2548752 -0.2123960 #E2E2FF
## 46 -0.2123960 -0.1699168 #E7E7FF
## 47 -0.1699168 -0.1274376 #ECECFF
## 48 -0.1274376 -0.0849584 #F2F2FF
## 49 -0.0849584 -0.0424792 #F7F7FF
## 50 -0.0424792 0.0000000 #FCFCFF
## 51 0.0000000 0.0424792 #FFFCFC
## 52 0.0424792 0.0849584 #FFF7F7
## 53 0.0849584 0.1274376 #FFF2F2
## 54 0.1274376 0.1699168 #FFECEC
## 55 0.1699168 0.2123960 #FFE7E7
## 56 0.2123960 0.2548752 #FFE2E2
## 57 0.2548752 0.2973544 #FFDDDD
## 58 0.2973544 0.3398336 #FFD8D8
## 59 0.3398336 0.3823128 #FFD3D3
## 60 0.3823128 0.4247920 #FFCECE
## 61 0.4247920 0.4672712 #FFC8C8
## 62 0.4672712 0.5097504 #FFC3C3
## 63 0.5097504 0.5522296 #FFBEBE
## 64 0.5522296 0.5947088 #FFB9B9
## 65 0.5947088 0.6371880 #FFB4B4
## 66 0.6371880 0.6796672 #FFAFAF
## 67 0.6796672 0.7221464 #FFA9A9
## 68 0.7221464 0.7646256 #FFA4A4
## 69 0.7646256 0.8071048 #FF9F9F
## 70 0.8071048 0.8495840 #FF9A9A
## 71 0.8495840 0.8920632 #FF9595
## 72 0.8920632 0.9345424 #FF9090
## 73 0.9345424 0.9770216 #FF8B8B
## 74 0.9770216 1.0195008 #FF8585
## 75 1.0195008 1.0619800 #FF8080
## 76 1.0619800 1.1044592 #FF7B7B
## 77 1.1044592 1.1469384 #FF7676
## 78 1.1469384 1.1894176 #FF7171
## 79 1.1894176 1.2318968 #FF6C6C
## 80 1.2318968 1.2743760 #FF6767
## 81 1.2743760 1.3168552 #FF6161
## 82 1.3168552 1.3593344 #FF5C5C
## 83 1.3593344 1.4018136 #FF5757
## 84 1.4018136 1.4442928 #FF5252
## 85 1.4442928 1.4867720 #FF4D4D
## 86 1.4867720 1.5292512 #FF4848
## 87 1.5292512 1.5717304 #FF4242
## 88 1.5717304 1.6142096 #FF3D3D
## 89 1.6142096 1.6566888 #FF3838
## 90 1.6566888 1.6991680 #FF3333
## 91 1.6991680 1.7416472 #FF2E2E
## 92 1.7416472 1.7841264 #FF2929
## 93 1.7841264 1.8266056 #FF2424
## 94 1.8266056 1.8690848 #FF1E1E
## 95 1.8690848 1.9115640 #FF1919
## 96 1.9115640 1.9540432 #FF1414
## 97 1.9540432 1.9965224 #FF0F0F
## 98 1.9965224 2.0390016 #FF0A0A
## 99 2.0390016 2.0814808 #FF0505
## 100 2.0814808 2.1239600 #FF0000
##
## $`GO:0040008`$layout
## $`GO:0040008`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0040008`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0040008`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0051726`
## $`GO:0051726`$rowInd
## [1] 85 133 16 45 99 132 48 105 76 21 140 52 55 116 96 50 17 128
## [19] 46 10 77 124 33 88 109 95 89 103 66 92 32 86 67 23 35 75
## [37] 44 108 104 24 5 79 18 72 101 3 87 53 14 26 100 136 112 39
## [55] 111 30 139 127 58 131 98 121 57 78 31 37 34 51 110 56 7 122
## [73] 2 107 106 6 28 126 81 19 135 27 69 74 42 43 125 29 65 138
## [91] 4 20 83 61 38 120 134 1 91 102 13 49 15 68 115 129 90 80
## [109] 97 82 73 118 113 60 93 25 36 12 94 64 11 54 119 8 70 9
## [127] 117 22 137 130 84 71 123 114 63 47 40 41 62 59
##
## $`GO:0051726`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0051726`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0051726`$carpet
## AT3G50000 AT5G61650 AT1G27630 AT2G18040 AT4G19600
## P11554_207 -1.16018750 -0.6762369 0.14747698 -0.27516193 -0.25477782
## P11554_208 -0.41095023 -0.6762369 0.39073518 0.04484604 -0.24066306
## P11554_209 0.20451150 -0.6762369 0.31208327 0.25475345 -0.46251849
## P11554_210 -1.44683019 -0.6762369 -0.34817162 -1.26423532 -0.92844848
## P11554_211 -1.20339737 -0.6762369 -0.03002233 -1.15349135 -1.02828287
## P11554_212 -0.37876146 -0.6762369 0.51282867 -1.45399091 -0.78349043
## P11554_213 0.13876202 1.3061125 -0.32932967 -0.24985020 0.01869556
## P11554_214 0.55702451 1.1429252 -1.20076351 -0.16074942 -0.28107285
## P11554_215 -0.04271474 -0.6762369 -0.29980703 0.18783666 -0.11191103
## P11554_216 -0.45803297 -0.6762369 -1.63710383 -1.04075925 -1.24544814
## P11554_217 0.15467100 1.1285955 -1.97301968 -0.97576982 -1.24050099
## P11554_218 0.15186512 -0.6762369 -1.23575799 -0.81592304 -1.05073886
## P11554_225 0.49672921 -0.6762369 0.53406628 1.11575394 0.94740403
## P11554_226 2.20693472 1.9933521 0.97590187 1.36090161 1.35147538
## P11554_227 2.17801544 1.1785206 1.90238590 1.53530417 1.43252628
## P11554_228 -1.10288806 -0.6762369 0.85398659 0.26854285 1.14688499
## P11554_229 -0.14989115 -0.6762369 0.67847930 1.19651714 1.25647988
## P11554_230 0.26514014 1.3653368 0.74603162 1.42547538 1.47438690
## AT5G61460 AT2G22010 AT4G37490 AT3G21870 AT1G47220 AT5G67380
## P11554_207 0.1690030 -0.06861385 -1.5354250 -0.593274 0.8495647 -0.7683708
## P11554_208 0.5745332 0.20512935 -0.2975766 -0.593274 0.9989809 -0.4959823
## P11554_209 0.4296886 -0.23228315 0.3193324 1.380750 -0.7614314 -0.7447125
## P11554_210 -1.1566688 -0.78179879 -0.1259733 -0.593274 -0.7614314 -1.0926322
## P11554_211 -1.3100682 -0.78677987 -0.5272018 1.581811 1.3632010 -0.5654162
## P11554_212 -0.9219234 -0.53977540 -0.3005791 -0.593274 -0.7614314 -0.5909952
## P11554_213 0.1434596 -0.50915673 -0.8766394 -0.593274 -0.7614314 -0.2852988
## P11554_214 0.3320849 0.27052089 0.6116538 1.823656 -0.7614314 -0.8509003
## P11554_215 0.2835217 -0.39345128 -0.2043430 -0.593274 -0.7614314 -0.5815864
## P11554_216 -1.6677165 -1.28954695 -0.3178121 -0.593274 -0.7614314 -0.8766509
## P11554_217 -1.4624459 -1.20022494 -1.3112611 -0.593274 -0.7614314 -0.7240461
## P11554_218 -1.2568870 -1.63614786 -1.5287794 -0.593274 0.8257927 -0.3937808
## P11554_225 0.9054863 1.28695770 1.5757732 -0.593274 1.3455171 1.1460560
## P11554_226 1.0073601 0.89586204 1.0773172 1.914987 1.6886488 1.5843314
## P11554_227 1.0946348 1.00235598 0.6717773 -0.593274 -0.7614314 1.7107005
## P11554_228 0.8349256 1.60905014 -0.2506158 1.011359 -0.7614314 0.8237013
## P11554_229 0.7664692 0.48918154 1.5685039 -0.593274 1.3040400 1.1710188
## P11554_230 1.2345427 1.67872117 1.4518489 -0.593274 -0.7614314 1.5345643
## AT2G26430 AT2G27960 AT5G22000 AT4G14220 AT2G23080
## P11554_207 -1.7459208 -1.02612106 -0.71969923 -0.25334034 -1.39657957
## P11554_208 -1.0512180 0.02624340 -0.43029242 -0.40018432 -1.04034844
## P11554_209 0.3004913 -0.40151646 0.76392231 0.44041176 -1.01623290
## P11554_210 -0.5247178 -0.05032417 -0.23571244 0.71708252 0.50490323
## P11554_211 -1.1026499 -0.14448016 -0.25415423 0.34757321 0.49091106
## P11554_212 -0.6386261 -0.17551821 -0.29940653 0.71782824 0.82795785
## P11554_213 -0.6220417 -1.24731273 -1.05936133 -2.66534199 -1.52576901
## P11554_214 -1.0581959 -1.40183359 -2.22351330 -1.55574679 -1.29709543
## P11554_215 -0.1027736 -1.72284836 -1.31615030 -1.32441492 -0.87694142
## P11554_216 -0.3862739 -0.15816120 -0.38724669 0.83193927 0.01608135
## P11554_217 0.4076203 -0.53995148 -0.05096494 -0.12556598 0.15936505
## P11554_218 -0.1280205 0.04255117 0.40821503 0.03690159 0.24331830
## P11554_225 0.5823014 0.88022870 0.14344025 0.40158951 0.06958938
## P11554_226 0.7879527 0.98822950 1.19251277 0.20947789 0.75903153
## P11554_227 1.7069688 1.86086711 1.41821162 1.23606136 0.89696507
## P11554_228 1.2894615 0.73717111 0.33959932 0.01711205 -0.02471837
## P11554_229 0.4871189 0.69475225 1.62251594 0.06227844 1.18526437
## P11554_230 1.7985235 1.63802417 1.08808415 1.30633847 2.02429794
## AT1G34460 AT5G48640 AT2G20580 AT1G14750 AT3G23580
## P11554_207 -0.93199178 -1.04072417 -1.11929270 -1.314156672 -0.28646242
## P11554_208 -0.60133724 -1.19910847 -0.91424775 -0.547558474 0.84570028
## P11554_209 -0.58308690 -0.98335185 -0.64039995 0.294893306 -0.40458334
## P11554_210 0.09492163 0.51298886 0.18659378 0.648454101 -0.19666603
## P11554_211 0.70207659 0.67750817 0.21981921 0.961171649 -0.53858578
## P11554_212 0.84080951 1.04905159 0.35133370 1.633524205 -0.09544559
## P11554_213 -1.52476760 -1.16073341 -1.32366814 0.009506058 -0.18193164
## P11554_214 -1.67517607 -1.86514394 -1.21978802 -1.188316776 -0.30886808
## P11554_215 -1.75632886 -1.32411200 -1.41770817 0.088360784 0.29669368
## P11554_216 0.36994794 0.64938323 -0.30305995 0.612056686 0.74369696
## P11554_217 0.70960521 0.56750363 -0.15942956 0.040589110 -0.39715550
## P11554_218 0.70117083 0.45430173 0.08206493 0.429170655 -0.14132834
## P11554_225 0.02066363 0.04359678 0.02962313 -2.512872642 -2.12617017
## P11554_226 0.66341246 -0.11675079 0.67639617 0.903809443 -1.01425145
## P11554_227 0.85900173 0.50381575 0.71730567 0.602581823 -0.84379847
## P11554_228 -0.49330902 0.71401652 1.28837928 -0.887194733 1.12235885
## P11554_229 1.12920648 1.58379968 1.75569682 0.654224632 1.05145614
## P11554_230 1.47518148 0.93395866 1.79038155 -0.428243157 2.47534091
## AT5G45190 AT1G73690 AT3G60550 AT5G07450 AT4G14150
## P11554_207 -1.483098611 0.5088373 0.5781832 -0.10498459 0.02290890
## P11554_208 0.148637149 1.1695896 1.3438869 0.02233586 0.69488222
## P11554_209 0.698661915 1.3752594 -0.8263181 0.10505007 -0.08306818
## P11554_210 0.432746813 1.2740239 -0.8263181 -0.70304603 -1.63241032
## P11554_211 0.253922787 0.4671904 -0.8263181 0.14003177 -0.04239288
## P11554_212 1.132546865 0.3774490 1.7096187 0.14000520 -0.49723616
## P11554_213 -0.001170315 0.2130767 0.7598300 0.21868667 1.06344358
## P11554_214 0.523908127 -0.2112003 0.6292581 -1.63877401 0.98024183
## P11554_215 -1.895935080 -0.9559733 -0.8263181 -0.13807204 1.62531557
## P11554_216 -1.198520307 -1.3449210 -0.8263181 -0.16142926 -0.64134538
## P11554_217 -0.922964825 -1.0784722 1.6743807 1.95933910 1.62283695
## P11554_218 -0.352680080 -0.7376110 0.5574582 0.78560589 0.69506375
## P11554_225 0.053227285 0.2438586 1.0105653 0.65619524 0.27660593
## P11554_226 -0.243605467 -2.1742626 -0.8263181 -2.75953113 -0.12102403
## P11554_227 -0.507106723 -0.7354943 -0.8263181 0.93509708 -1.11460894
## P11554_228 -0.075370450 0.8359823 -0.8263181 0.07835858 -0.02089426
## P11554_229 1.369671398 0.9576685 -0.8263181 0.52830339 -1.39422649
## P11554_230 2.067129520 -0.1850010 -0.8263181 -0.06317179 -1.43409208
## AT3G63120 AT4G34160 AT2G44740 AT4G03270 AT1G70210
## P11554_207 -0.2722386 0.005670564 0.07474432 0.75751400 1.28499699
## P11554_208 -0.3746982 -0.015473030 0.06630093 0.51696786 1.09522654
## P11554_209 -0.1218671 -0.035845268 0.20135161 0.70690708 0.50632874
## P11554_210 -0.8646246 -0.338371887 -0.85507389 1.05453600 0.99625142
## P11554_211 -0.5131288 -0.274964576 -0.92124385 -1.47602783 0.44631589
## P11554_212 -0.1099655 -0.418550803 -1.05724080 -1.47602783 0.66252391
## P11554_213 2.1711651 1.358685339 1.65551887 0.58367332 -0.73465239
## P11554_214 1.3871338 1.482018215 1.12502116 -1.47602783 -0.87007513
## P11554_215 1.5962102 1.507218219 1.35981463 0.46247955 -0.30133401
## P11554_216 1.0519375 1.057337702 1.45675094 1.25355215 1.36456590
## P11554_217 0.2942978 1.156017018 0.59172124 0.82047496 0.56979829
## P11554_218 0.8270841 0.934361430 0.78889426 0.72456962 0.28680618
## P11554_225 -0.6367489 -1.156178697 0.07117331 0.21086377 -0.06135774
## P11554_226 -0.4880779 -1.119046519 -0.75416174 0.48558615 -0.75105952
## P11554_227 -1.1649095 -0.841564978 -0.04773249 -1.47602783 -0.38360319
## P11554_228 -1.1458255 -1.293229391 -1.21333939 -0.22110582 -1.06151588
## P11554_229 -0.6894172 -0.950236586 -1.16803774 -1.47602783 -0.49624931
## P11554_230 -0.9463267 -1.057846751 -1.37446137 0.02412052 -2.55296673
## AT3G50070 AT2G45080 AT1G50240 AT1G76310 AT3G20150 AT2G17620
## P11554_207 0.20079650 0.2822414 -0.08751811 0.07300656 0.4504544 0.8748714
## P11554_208 0.49813288 0.1071033 0.64935806 0.57094205 0.6412934 0.7389339
## P11554_209 0.01380268 0.2144466 0.68484050 1.22577864 0.1301460 0.1068920
## P11554_210 0.71283662 0.5368599 0.11043846 0.11095866 1.2582951 0.9197302
## P11554_211 1.01333434 1.4025988 0.40245607 0.39996738 -0.1985455 0.6338477
## P11554_212 0.39083946 0.1014876 0.37674859 0.37109999 0.7291742 0.8807667
## P11554_213 0.40970262 0.1254039 0.76813298 0.83645301 0.1853557 0.1167484
## P11554_214 0.14109163 0.4940920 0.85666416 0.63365559 0.8706169 0.5086589
## P11554_215 -0.28456606 1.0990688 0.77533929 1.04356341 1.0733422 0.1802182
## P11554_216 1.51251815 1.5715490 1.08648986 0.43332152 0.6032732 1.0272144
## P11554_217 1.40662320 0.9670248 0.96786955 0.89755964 0.9489563 0.9258818
## P11554_218 1.14488180 0.0192316 0.94345103 0.99559348 0.6801133 0.8424683
## P11554_225 -1.25921105 -1.5760560 -1.96266255 -1.18083838 -2.0004966 -1.5421722
## P11554_226 -1.14896918 -1.7793381 -1.63877405 -1.66022309 -1.5443865 -1.0348306
## P11554_227 -1.70277969 -1.6185990 -1.04281336 -0.77253400 -1.4474843 -0.8330483
## P11554_228 -1.34557863 -0.3710423 -1.29195009 -1.76593218 -1.1324175 -1.0119247
## P11554_229 -0.61597610 -0.5950755 -0.42350696 -0.67721335 -0.6257899 -1.6453350
## P11554_230 -1.08747916 -0.9809969 -1.17456343 -1.53515894 -0.6219003 -1.6889211
## AT5G06150 AT4G35620 AT1G53140 AT1G05440 AT3G23890 AT1G44110
## P11554_207 0.9820362 1.0759684 0.39175714 0.6913499 0.4747263 0.93283443
## P11554_208 0.8137129 0.8378269 0.78179429 1.0107677 1.2923942 1.35918495
## P11554_209 0.5828501 0.3696383 0.43484096 1.4406834 0.9777198 1.05602781
## P11554_210 0.5191027 0.4769892 0.22532923 0.9525019 0.4539379 0.62617353
## P11554_211 0.4330203 0.5977430 -0.00813146 0.5252172 0.1975577 0.42756483
## P11554_212 0.3746919 0.8777562 0.95345150 -0.1010815 0.4311020 0.32853271
## P11554_213 0.7399072 0.3738371 1.11920677 1.3052538 0.6447525 0.47831372
## P11554_214 0.5523373 0.9277422 1.06008994 0.2793860 1.1789711 1.07093151
## P11554_215 0.3173754 -0.0385376 0.45497863 0.2978220 0.6397487 0.46625017
## P11554_216 0.8922405 0.9699053 1.00133897 0.2821980 0.6002678 0.70911173
## P11554_217 0.9287031 0.7714122 1.01435747 0.5395334 0.6567489 0.15044727
## P11554_218 0.9168378 0.4789071 0.21395967 0.2336478 0.3635734 0.09817155
## P11554_225 -1.4508674 -0.8174181 -1.36682438 -0.9852936 -1.4533920 -1.02018349
## P11554_226 -1.3768268 -1.3844367 -1.14082651 -1.4383497 -1.4584113 -1.56596547
## P11554_227 -1.1983138 -1.1313941 -0.99607502 -1.0729914 -1.0705713 -0.97802545
## P11554_228 -1.4763080 -1.5939270 -1.59591057 -0.9503456 -1.2887196 -1.55503602
## P11554_229 -1.0351244 -0.8583330 -0.78051764 -1.8992611 -1.4728318 -1.01909161
## P11554_230 -1.5153750 -1.9336793 -1.76281900 -1.1110385 -1.1675742 -1.56524216
## AT3G11520 AT4G26660 AT1G03780 AT3G51280 AT2G26760 AT1G20610
## P11554_207 0.9046195 0.5097368 0.53760813 0.8898906 0.98997545 1.21855586
## P11554_208 1.1769606 1.0777019 0.75933169 0.8113518 1.37354037 1.54107242
## P11554_209 0.6403287 0.6283999 0.81923249 0.9767962 0.92667582 1.19361182
## P11554_210 0.3683880 0.1225244 0.03242994 0.2308941 0.13681106 0.23635286
## P11554_211 0.4774566 0.2638093 0.39711162 0.2257577 0.70537668 0.14332966
## P11554_212 0.6251957 0.5613660 0.75816240 0.4075570 0.41386539 0.84293901
## P11554_213 0.3955908 0.7229974 0.85744856 0.7921499 0.36547599 0.48210535
## P11554_214 1.0186098 1.0105923 0.66439273 1.0060805 1.17768185 0.91791948
## P11554_215 0.7339342 0.6757324 0.98226037 0.8636822 0.54578135 0.55853687
## P11554_216 0.3139828 0.9693917 0.93583105 0.7799263 -0.02996059 0.03830312
## P11554_217 0.7579921 0.5125464 0.71227313 0.2210682 0.36841516 0.36458906
## P11554_218 0.4839872 0.8885172 0.56033352 0.7783524 0.58988620 -0.37310024
## P11554_225 -0.7515595 -1.3182256 -1.25754505 -1.4143286 -1.16890803 -1.58935161
## P11554_226 -1.5839100 -1.0794040 -1.39697666 -1.1902208 -0.66701574 -0.92201457
## P11554_227 -1.4797216 -1.1266223 -1.01536198 -1.3437654 -1.01957122 -0.71164625
## P11554_228 -1.3994955 -1.5512432 -1.40545682 -1.2450464 -1.73404002 -1.28876939
## P11554_229 -1.0475286 -1.2092823 -1.35447664 -1.3195668 -1.44178399 -1.00467607
## P11554_230 -1.6348309 -1.6585383 -1.58659848 -1.4705789 -1.53220571 -1.64775738
## AT1G59540 AT4G21820 AT5G63950 AT5G10440 AT1G80370
## P11554_207 0.89838602 0.3961242 0.24195515 0.36264158 0.59868208
## P11554_208 0.90761152 0.8168150 1.75196736 0.51785005 0.60517738
## P11554_209 0.85293264 0.9295113 1.20202743 1.90369639 2.08708660
## P11554_210 -0.21382820 0.0488946 -0.08229845 -0.47880735 0.76087921
## P11554_211 -0.18095297 0.3247095 0.41721309 -2.10707586 -0.57376766
## P11554_212 0.13412257 0.1906130 0.08753884 0.31694616 0.50654728
## P11554_213 1.09666630 1.5870220 0.42581077 -0.84710464 0.30893992
## P11554_214 1.77799150 1.2574531 0.45992408 0.29152589 0.57361981
## P11554_215 0.92163613 0.9007700 1.05492810 2.16196719 0.77315241
## P11554_216 0.63155658 0.1953830 -0.12780162 0.61018777 -1.26109231
## P11554_217 0.33528696 0.6154065 0.34619345 -0.22876546 -0.04326273
## P11554_218 -0.06332676 0.2466365 0.26118091 -0.14000334 0.45252299
## P11554_225 -1.31176673 -1.6206249 -2.29152000 0.04471264 -1.41768096
## P11554_226 -0.83269463 -0.9055910 -1.81331732 -0.65112221 -0.22501959
## P11554_227 -1.43072396 -1.0444621 -1.10107850 0.13036454 -0.40643614
## P11554_228 -1.52820159 -1.1091011 -0.36245902 -0.68033377 -0.77836397
## P11554_229 -0.87351120 -1.4783175 -0.75237006 -0.03237705 0.28069748
## P11554_230 -1.12118416 -1.3512421 0.28210578 -1.17430253 -2.24168178
## AT5G09790 AT1G68310 AT5G67260 AT5G48630 AT2G31320
## P11554_207 0.62625910 0.84139146 0.16770684 2.009509945 0.6746070
## P11554_208 -0.14761359 0.86967773 0.62003491 0.816960411 0.7602131
## P11554_209 1.49238745 1.55849836 0.79427538 0.691072928 1.4915479
## P11554_210 -0.54491353 -0.32151871 -0.19736573 -1.093407231 -1.7181133
## P11554_211 -0.34871482 -0.59454483 0.54270955 -0.480111824 -0.5416318
## P11554_212 -0.52313099 -0.88258337 -0.91962906 -0.510341823 -0.2930092
## P11554_213 1.31065067 0.52459402 0.48356712 0.629086207 2.0062609
## P11554_214 -0.01741395 1.41074721 1.59334443 1.140854879 0.9813375
## P11554_215 2.06267110 1.80995000 2.41155440 1.640009515 1.1176996
## P11554_216 -1.09266850 -0.82920263 -1.26881538 -0.727769109 -1.6263809
## P11554_217 -0.95564998 -1.41411033 -0.97239779 -1.282451561 -0.4775084
## P11554_218 -0.36067895 -0.96117382 -1.12879120 -0.860954698 -0.9091896
## P11554_225 -0.28194034 -0.51624560 -0.45693272 -0.622501960 -0.2039350
## P11554_226 -1.16120660 -0.01750975 0.53611587 0.439846310 -0.1909670
## P11554_227 -0.69146531 -0.23124104 -0.50190041 0.163506510 0.0143302
## P11554_228 1.15319615 -1.52776915 -1.17356446 -1.364339397 -0.3172102
## P11554_229 0.76130000 0.25157872 -0.04840687 -0.598863126 -0.3936088
## P11554_230 -1.28106793 0.02946170 -0.48150486 0.009894024 -0.3744421
## AT5G57590 AT4G19560 AT5G40840 AT2G31270 AT3G23740 AT1G69770
## P11554_207 0.33077296 0.4562264 0.4397473 1.3302474 1.3396367 1.2168231
## P11554_208 1.01305315 1.2952824 1.0317361 1.1977920 1.1426616 1.1287121
## P11554_209 1.38282436 1.5855190 0.7239700 1.0730228 1.1358363 1.1008244
## P11554_210 -1.10749373 -1.1465668 -0.5151019 -0.3970551 -0.4354116 -0.4566175
## P11554_211 -0.13079827 -0.2751132 -1.0933676 -0.4924679 -0.4941302 -0.5338723
## P11554_212 -0.15301050 -1.0253843 0.4028398 -0.3826736 -0.5087725 -0.5311471
## P11554_213 0.83317607 0.6887389 1.1733657 1.4371205 1.4679987 1.5417596
## P11554_214 1.41155987 1.7808829 1.5363580 1.4683452 1.5345695 1.5372370
## P11554_215 1.89383227 0.3766625 2.1039031 1.5002337 1.4725056 1.5402341
## P11554_216 -1.86180614 -0.6860718 -0.4173033 -0.4672640 -0.5500514 -0.4820198
## P11554_217 -0.62143861 -1.2303247 0.1812927 -0.6042890 -0.6059442 -0.5217882
## P11554_218 -1.01978238 -0.2212008 -0.9112168 -0.5407428 -0.5229375 -0.5244628
## P11554_225 0.03681596 0.3554095 -0.4021719 -0.5467487 -0.5575552 -0.6429901
## P11554_226 -0.63700616 -1.4167558 -0.6784010 -0.6233182 -0.7679564 -0.6681518
## P11554_227 0.30780827 1.0403819 -0.8566529 -0.6736884 -0.7013962 -0.6942066
## P11554_228 -0.71739796 -0.1036497 -0.5725964 -1.0264521 -0.9312076 -0.9726310
## P11554_229 -0.62354879 -0.6266338 -1.5242118 -1.2234305 -1.0113743 -1.0494889
## P11554_230 -0.33756039 -0.8474026 -0.6221891 -1.0286311 -1.0064714 -0.9882142
## AT1G78650 AT1G75150 AT2G24490 AT5G08020 AT2G29680 AT1G07370
## P11554_207 1.4141495 1.3328203 1.3906610 1.3098072 1.3123103 1.2479632
## P11554_208 1.0282194 1.3263445 1.2687255 1.2122490 1.2607842 1.2638634
## P11554_209 1.1333030 1.1951879 1.2807546 1.2485153 1.3347890 1.2012186
## P11554_210 -0.5104543 -0.6074271 -0.5998294 -0.6317226 -0.6985314 -0.7477878
## P11554_211 -0.6447993 -0.6300011 -0.5995103 -0.5633658 -0.6079118 -0.6799448
## P11554_212 -0.3538967 -0.4453156 -0.5244005 -0.5783329 -0.5990920 -0.5499127
## P11554_213 1.4892314 1.3633436 1.3542183 1.3925527 1.3951124 1.5383430
## P11554_214 1.4055897 1.5602290 1.3539319 1.4851550 1.4117129 1.4048909
## P11554_215 1.6149815 1.3980083 1.4659468 1.4855806 1.4315581 1.4694567
## P11554_216 -0.8162330 -0.6435570 -0.6457795 -0.5645983 -0.5608253 -0.5358026
## P11554_217 -0.6020175 -0.6711028 -0.4058549 -0.6002815 -0.5752535 -0.5539846
## P11554_218 -0.6038185 -0.7054308 -0.4858176 -0.5847791 -0.5395682 -0.5138255
## P11554_225 -0.8077796 -0.5713384 -0.6618007 -0.4472875 -0.5844514 -0.6093448
## P11554_226 -0.5920079 -0.6205128 -0.5631934 -0.5694748 -0.5384633 -0.5576318
## P11554_227 -0.4520264 -0.6869229 -0.6241822 -0.6568106 -0.5200568 -0.5070446
## P11554_228 -0.9560058 -0.8372961 -0.9212376 -0.9987128 -0.9268903 -1.0253172
## P11554_229 -0.9621202 -0.7478257 -0.9274583 -0.9780567 -0.9157106 -0.8042870
## P11554_230 -0.7843153 -1.0092033 -1.1551737 -0.9604372 -1.0795122 -1.0408525
## AT5G43080 AT1G02970 AT5G02520 AT4G37630 AT1G07270 AT1G67320
## P11554_207 1.5053354 1.1895016 1.3095250 1.2815772 1.1565064 1.3475981
## P11554_208 1.3531769 1.0402703 1.3714185 1.3514580 1.4898554 1.3123250
## P11554_209 1.1015110 1.1932780 1.3639613 1.1464008 1.2629070 1.4930854
## P11554_210 -0.6081216 -0.6194429 -0.5063147 -0.4592652 -0.3041721 -0.5616834
## P11554_211 -0.6275332 -0.5887447 -0.3262023 -0.4805167 -0.7005725 -0.4360939
## P11554_212 -0.5034924 -0.3951856 -0.1291863 -0.4058663 -0.4667231 -0.3557620
## P11554_213 1.2535882 1.6631276 1.1536365 1.1943414 1.5208519 1.3815020
## P11554_214 1.2715294 1.1924788 1.1323069 1.7085906 1.3455930 1.2487143
## P11554_215 1.6005143 1.6693528 1.5778187 1.2693137 1.2250741 1.2998709
## P11554_216 -0.4821917 -0.5408598 -0.5578037 -0.4994367 -0.3937957 -0.6215555
## P11554_217 -0.5366754 -0.6340409 -0.3368507 -0.8038876 -0.4408790 -0.5636698
## P11554_218 -0.4806124 -0.8083424 -0.8315809 -0.5562516 -0.6006485 -0.4518079
## P11554_225 -0.5795354 -0.1846441 -0.8509071 -0.4219436 -0.5598631 -0.6946568
## P11554_226 -0.6251193 -0.5747512 -0.6355880 -0.5249162 -0.4686905 -0.5929288
## P11554_227 -0.7294767 -0.5237745 -0.5099174 -0.4598810 -0.8448752 -0.7258497
## P11554_228 -1.0117148 -1.0744005 -0.9570335 -0.9514355 -1.0707538 -1.1195479
## P11554_229 -0.7488276 -1.1877300 -1.3228988 -1.3084272 -1.1373349 -0.9674317
## P11554_230 -1.1523545 -0.8160923 -0.9443836 -1.0798539 -1.0124794 -0.9921084
## AT5G48600 AT3G24495 AT1G44900 AT5G63920 AT1G65470 AT3G02820
## P11554_207 1.1850839 1.1759085 1.2871712 1.1110978 1.2274634 1.3577399
## P11554_208 1.4112412 1.3129506 1.3404583 1.3349649 1.3571820 1.2717266
## P11554_209 1.2979243 1.3620853 1.3362781 1.4055262 1.2213711 1.3521512
## P11554_210 -0.4601231 -0.5086609 -0.5291033 -0.5359858 -0.6839690 -0.5841437
## P11554_211 -0.5431664 -0.5744437 -0.4760306 -0.5269688 -0.4848924 -0.4482701
## P11554_212 -0.3626244 -0.3793020 -0.3959850 -0.3857805 -0.3272211 -0.4300846
## P11554_213 1.3788438 1.4568398 1.3619726 1.3414047 1.3716821 1.2426448
## P11554_214 1.3865620 1.3683543 1.3705471 1.5132862 1.3518045 1.2829005
## P11554_215 1.4561109 1.4233484 1.3836663 1.3596463 1.5727082 1.6006804
## P11554_216 -0.6694035 -0.4544018 -0.5496704 -0.5300699 -0.5335871 -0.5122108
## P11554_217 -0.5402411 -0.6087522 -0.5200249 -0.5065896 -0.5595543 -0.5807392
## P11554_218 -0.5947747 -0.5533049 -0.4627397 -0.4046068 -0.6284792 -0.5199123
## P11554_225 -0.8902324 -0.7099810 -0.6518325 -0.7656418 -0.6492096 -0.7635414
## P11554_226 -0.6540643 -0.6408921 -0.6598547 -0.6934622 -0.6164777 -0.6878525
## P11554_227 -0.5556733 -0.6273739 -0.6669496 -0.6733024 -0.6416414 -0.6298736
## P11554_228 -1.0114518 -0.9496034 -1.0508446 -1.1549999 -0.9253341 -0.9879674
## P11554_229 -0.9858013 -1.0748779 -1.1373090 -1.0363476 -1.0217611 -1.0343790
## P11554_230 -0.8482098 -1.0178932 -0.9797493 -0.8521707 -1.0300845 -0.9288688
## AT3G18524 AT2G07690 AT2G16440 AT5G46280 AT1G67630 AT2G40550
## P11554_207 1.0813158 1.2655021 1.3113914 1.2840035 1.2757878 1.2249216
## P11554_208 1.1793649 1.3002909 1.3040662 1.4012114 1.4147095 1.3475759
## P11554_209 1.4516359 1.3194267 1.3335481 1.3744306 1.4695292 1.3859945
## P11554_210 -0.8033740 -0.5730487 -0.5938695 -0.6071882 -0.5756564 -0.5440521
## P11554_211 -0.5294062 -0.4611332 -0.5494372 -0.5419400 -0.5893138 -0.4626213
## P11554_212 -0.5323576 -0.4526048 -0.4580354 -0.5738425 -0.5027818 -0.4651035
## P11554_213 1.4989032 1.3919045 1.3351264 1.2893939 1.3049248 1.4201793
## P11554_214 1.4934262 1.3761327 1.3690947 1.3415019 1.3345465 1.3664964
## P11554_215 1.3899007 1.4379469 1.4326163 1.4349610 1.3331947 1.3784274
## P11554_216 -0.6131065 -0.6274699 -0.5596894 -0.4993116 -0.6739194 -0.6441591
## P11554_217 -0.6217976 -0.6364002 -0.5850843 -0.5836650 -0.6655967 -0.6092271
## P11554_218 -0.4505602 -0.5643704 -0.5587570 -0.6696976 -0.6449196 -0.6045223
## P11554_225 -0.4662589 -0.6369667 -0.5280021 -0.5530158 -0.5866447 -0.6404719
## P11554_226 -0.6184495 -0.4483940 -0.5363683 -0.5130034 -0.4694051 -0.5461576
## P11554_227 -0.5257315 -0.5542377 -0.5143661 -0.5526989 -0.4650593 -0.5904035
## P11554_228 -1.0109729 -1.0898288 -1.0980923 -0.9780033 -0.9482895 -0.9862954
## P11554_229 -0.9981995 -1.0890666 -1.1200221 -1.0929475 -1.0463365 -1.0823209
## P11554_230 -0.9243323 -0.9576831 -0.9841195 -0.9601884 -0.9647698 -0.9482602
## AT5G67100 AT1G04020 AT1G47210 AT3G42660 AT2G36010 AT1G78770
## P11554_207 1.2755957 1.2353125 1.4047305 1.2026529 1.0097221 1.0911893
## P11554_208 1.3579576 1.5066604 1.2574210 1.3543728 1.3123304 1.3025314
## P11554_209 1.3466087 1.3197322 1.2000855 1.3296797 1.3589766 1.3054000
## P11554_210 -0.5541215 -0.5553537 -0.4656200 -0.5845479 -0.5384603 -0.3948275
## P11554_211 -0.4842312 -0.5376793 -0.4641946 -0.5147894 -0.4909508 -0.4746138
## P11554_212 -0.5097906 -0.3272224 -0.4518213 -0.4083394 -0.3431337 -0.4556716
## P11554_213 1.3860082 1.3941574 1.3188821 1.3344438 1.4484702 1.1728965
## P11554_214 1.3966324 1.2652945 1.4312309 1.3634470 1.4076514 1.4445825
## P11554_215 1.3700702 1.3481022 1.3743743 1.4178038 1.4692128 1.6174674
## P11554_216 -0.6628502 -0.6211426 -0.5567971 -0.6261368 -0.5164869 -0.7129891
## P11554_217 -0.7122248 -0.4642956 -0.4882648 -0.4915054 -0.4600681 -0.4645472
## P11554_218 -0.6151783 -0.6393611 -0.5703609 -0.5518063 -0.8505380 -0.4224507
## P11554_225 -0.5853395 -0.5276174 -0.5424781 -0.4524528 -0.5942850 -1.3014420
## P11554_226 -0.5107188 -0.6921307 -0.5066524 -0.4968942 -0.6997243 -0.4293049
## P11554_227 -0.5215794 -0.5540415 -0.4542843 -0.4386445 -0.4136425 -0.4588290
## P11554_228 -0.9402319 -1.0436733 -1.0886980 -1.0858299 -1.2480651 -1.1003175
## P11554_229 -1.0767945 -0.9737596 -1.2282493 -1.1435044 -0.7875248 -1.0351118
## P11554_230 -0.9598120 -1.1329821 -1.1693039 -1.2079490 -1.0634841 -0.6839622
## AT5G27680 AT5G62410 AT1G01370 AT4G02460 AT4G29170 AT1G18040
## P11554_207 1.1834485 0.9984663 1.0774924 1.1040710 1.1230335 0.9651769
## P11554_208 1.2818980 1.1344067 0.9760469 1.1458063 1.0781275 0.4599297
## P11554_209 0.9135632 1.2260337 1.3844050 1.5061699 1.3429584 1.2333857
## P11554_210 -0.4657243 -0.5818279 -0.2086459 -0.2466275 -0.3455657 -0.8430072
## P11554_211 -0.3532702 -0.4330440 -0.5515003 -0.3151451 -0.3200179 -0.3190267
## P11554_212 -0.4168482 -0.3687862 -0.5661568 -0.2866156 -0.5021045 -0.1798146
## P11554_213 1.3920407 1.1374980 1.6468283 1.3806348 1.3685896 1.6969431
## P11554_214 1.8553264 1.6968836 1.1982197 1.3223978 1.1870458 1.3690402
## P11554_215 1.3698353 1.6769697 1.6721586 1.4811517 1.8202573 1.8642781
## P11554_216 -0.6733442 -0.7732624 -0.5492081 -0.6866920 -0.5405523 -0.7070610
## P11554_217 -0.5151958 -0.1240111 -0.4413494 -0.4625901 -0.7108738 -0.5775239
## P11554_218 -0.5786198 -0.3218926 -0.5609742 -0.5323456 -0.2268326 -0.6437992
## P11554_225 -0.9045288 -0.7931206 -0.8324846 -0.9644814 -0.7950664 -0.1387249
## P11554_226 -0.6522701 -0.6897992 -0.9305390 -0.9143301 -0.7883706 -0.7747897
## P11554_227 -0.6952287 -0.6167416 -0.5722250 -0.5973125 -0.6527395 -0.6655631
## P11554_228 -1.0737888 -1.0435267 -1.1861148 -1.2898066 -0.8788921 -1.3750011
## P11554_229 -0.9479239 -1.1572843 -0.6316731 -0.7971661 -1.2688503 -0.9367031
## P11554_230 -0.7193694 -0.9669614 -0.9242798 -0.8471189 -0.8901463 -0.4277392
## AT2G22490 AT1G22270 AT2G45280 AT5G20850 AT5G49010 AT4G02070
## P11554_207 1.3144516 1.06824591 1.30985874 1.2344818 1.3188876 1.1926144
## P11554_208 1.2748486 1.58755775 1.49233275 1.3573137 1.5060545 1.4781713
## P11554_209 1.3269560 0.95597758 1.47949415 1.3126489 1.1701549 1.4298551
## P11554_210 -0.7694982 -0.98288870 -0.59761362 -0.6501801 -0.5408709 -0.7665759
## P11554_211 -0.9951765 -0.95089199 -0.84300695 -0.8350804 -0.5636194 -0.3843178
## P11554_212 -0.8502410 -0.72936634 -0.67858027 -0.8636645 -0.4222908 -0.5456866
## P11554_213 1.1407099 1.65510672 1.20630862 1.3191133 1.3280741 1.2985871
## P11554_214 1.0778910 1.31220758 1.25375319 1.5837739 1.1839520 1.3495335
## P11554_215 1.3467505 1.24789252 1.22791326 1.2564353 1.4467240 1.2721459
## P11554_216 -0.8905908 -0.63674531 -0.98461362 -0.7496484 -0.6514836 -0.7263330
## P11554_217 -1.0292782 -0.61475576 -0.87258857 -0.6992725 -0.9014903 -0.8289585
## P11554_218 -0.9225590 -0.86461862 -0.68009370 -0.9737973 -0.6166682 -0.6638184
## P11554_225 0.1286944 -0.32366601 -0.26523366 -0.3502298 -0.6951958 -0.3241191
## P11554_226 0.2185094 -0.03141229 -0.07700316 -0.2635790 -0.2053196 -0.4107060
## P11554_227 0.3045108 -0.31406875 -0.25928487 -0.3659977 -0.1685324 -0.3772035
## P11554_228 -1.0825456 -0.80103748 -0.79753763 -0.6711928 -1.1545816 -0.9678112
## P11554_229 -0.7666137 -0.35140028 -0.94452627 -1.0387349 -1.0589173 -1.2676605
## P11554_230 -0.8268191 -1.22613653 -0.96957839 -0.6023894 -0.9748771 -0.7577167
## AT3G24320 AT4G18470 AT3G27060 AT3G12280 AT5G25380 AT5G11300
## P11554_207 1.1626967 1.2848857 1.3315667 1.2180682 1.44875190 1.049002387
## P11554_208 1.1384927 1.3626590 1.4427012 1.3145524 1.51760819 1.197944880
## P11554_209 1.2889553 1.4616110 1.3968832 1.4049859 1.33295605 1.659417336
## P11554_210 -0.6203197 -0.4160826 -0.6069181 -0.4692371 -1.21369542 -0.411449502
## P11554_211 -0.5563531 -0.6076801 -0.5930519 -0.3220217 0.41226075 -0.214740878
## P11554_212 -0.5280890 -0.4224114 -0.5880054 -0.3519301 0.24325734 0.005289071
## P11554_213 1.4706251 1.3902503 1.3678835 1.3580634 0.91752489 0.726644737
## P11554_214 1.5187300 1.3156359 1.3365121 1.3919969 1.00433331 0.971705203
## P11554_215 1.3622487 1.2654145 1.2770265 1.3784434 -0.24668989 -0.467171190
## P11554_216 -0.8119189 -0.8030250 -0.8297179 -0.9213681 -0.43313901 -0.051925246
## P11554_217 -1.0623907 -0.5667648 -0.8827988 -0.9095040 -0.28212550 -0.126494571
## P11554_218 -0.6925845 -0.9083230 -0.8700503 -0.8889345 -0.82193795 -0.406208957
## P11554_225 -0.2085169 -0.3749001 -0.3969610 -0.6024969 0.01869071 0.434876032
## P11554_226 -0.3614163 -0.5303188 -0.4347964 -0.4490950 -0.51314465 -0.168788659
## P11554_227 -0.1504663 -0.5003786 -0.4741663 -0.4573603 -0.12271563 0.781527549
## P11554_228 -0.9647043 -0.9342504 -0.8101530 -0.9310099 -0.45024097 -2.093883964
## P11554_229 -1.1093620 -1.0330027 -0.8362733 -0.9890961 -2.36255696 -1.093053219
## P11554_230 -0.8756267 -0.9833190 -0.8296808 -0.7740564 -0.44913719 -1.792691008
## AT2G33560 AT4G04950 AT1G57820 AT1G77390 AT1G16330 AT4G09140
## P11554_207 1.41126316 1.0501997 0.3595012 0.8386156 0.9863955 1.16432028
## P11554_208 1.50262609 1.7546343 0.9980755 1.0513046 0.9223249 0.61578952
## P11554_209 1.81226306 1.6901801 1.3659949 0.4720732 0.2981498 0.53412202
## P11554_210 -0.42725931 -1.0713118 -0.7097144 -0.2740401 -0.7236422 -0.51952220
## P11554_211 0.09459429 -0.1814777 -0.7075302 -0.3083121 -0.7764358 -0.34298695
## P11554_212 -0.08948436 -0.8767922 -0.4287885 -0.8286207 0.1192896 -0.01888032
## P11554_213 0.37661873 0.7460613 1.3732173 1.4200670 1.6408418 2.24052600
## P11554_214 1.62539221 0.9448484 1.5306195 1.2569091 1.4490535 0.20238236
## P11554_215 0.14287436 0.9753433 1.2481212 2.0862405 1.4379631 1.75040033
## P11554_216 -0.84053714 -1.2743167 -0.2094874 -0.1488586 0.3021918 -0.32366186
## P11554_217 -0.23596231 -0.3604643 0.2428382 0.3711603 0.2563161 -0.71529881
## P11554_218 -0.24844953 -0.2962092 0.4524641 -0.1369152 0.3550813 0.50092426
## P11554_225 -0.42952754 0.2753321 -1.7248064 -1.0846331 -0.9882828 -1.34854710
## P11554_226 -0.37928451 -0.1784720 -0.9743803 -0.7793951 -1.3452959 -1.25569272
## P11554_227 -0.80138412 -0.2739323 -1.3859117 -0.8982927 -1.3032496 -0.74095895
## P11554_228 -1.77048589 -1.6438301 -0.8391944 -1.2010182 -0.9006643 -1.20093724
## P11554_229 -0.78818758 -0.4579440 -0.2596083 -1.2822556 -0.7906631 -0.08886322
## P11554_230 -0.95506960 -0.8218490 -0.3314103 -0.5540290 -0.9393737 -0.45311541
## AT2G40030 AT1G15570 AT2G27040 AT5G27620 AT1G09450
## P11554_207 0.56608029 0.46064213 0.41763475 0.9342171 1.14067060
## P11554_208 0.05880319 0.43332867 0.80432846 0.9146160 1.01761081
## P11554_209 1.51715672 0.84901891 0.97810208 0.8259398 0.45465578
## P11554_210 -0.27870976 -0.59369843 -0.80293132 -0.3851983 -0.89141769
## P11554_211 -0.22305292 -0.24856361 -0.64779678 -0.3171089 -0.09576789
## P11554_212 -0.18699911 0.23607132 -0.42616786 -0.3382805 -0.22788708
## P11554_213 1.89461381 1.93357696 1.79610316 1.9128809 1.65709160
## P11554_214 1.29780657 0.98546148 1.49547662 1.5621178 1.79001639
## P11554_215 1.44326073 1.66799152 1.67298644 1.5064889 1.55472045
## P11554_216 -0.36682827 -0.18805666 -0.33735093 -0.6337651 -0.31097454
## P11554_217 0.15263407 0.04374320 0.24673487 -0.4041156 -0.65062580
## P11554_218 0.36237603 0.01812318 -0.07633598 -0.7555659 -0.34015336
## P11554_225 -0.90909401 -0.27234408 -0.57290586 -0.4006308 -0.63725106
## P11554_226 -0.97545577 0.02800932 -0.37937398 -0.7261356 -1.21314308
## P11554_227 -0.89783312 -0.71080782 -0.36750535 -0.2745270 -0.76254832
## P11554_228 -1.12269707 -1.58582312 -1.17399648 -1.0018850 -0.91513172
## P11554_229 -1.13351249 -1.29075487 -1.09200549 -1.0551291 -0.59930136
## P11554_230 -1.19854889 -1.76591812 -1.53499634 -1.3639189 -0.97056373
## AT3G03130 AT1G10780 AT5G24330 AT1G47230 AT5G65420 AT5G55820
## P11554_207 1.3152889 0.96366371 1.2888296 1.3625787 1.3614326 0.83872398
## P11554_208 1.1753497 1.21572310 1.2043172 0.9566839 1.2182583 1.40167700
## P11554_209 1.0348202 1.01234774 1.0544269 0.7367921 0.7799337 0.82040360
## P11554_210 -0.5309712 -0.42377848 -0.1860195 -0.4134364 -0.6033322 -0.76294370
## P11554_211 -0.1364929 -0.32679299 -0.4073640 -0.2504996 -0.1943297 -0.26969501
## P11554_212 -0.0760110 -0.49900215 -0.3820900 -0.3048093 -0.2082269 -0.12026279
## P11554_213 1.5018049 1.81006236 1.4167994 1.5868203 1.3673075 1.41175653
## P11554_214 1.2950956 1.46552387 1.3931708 1.4734989 1.5599598 1.52272518
## P11554_215 1.2593250 1.26056609 1.5193153 1.5342216 1.2934116 1.40333433
## P11554_216 -0.1838422 -0.06356344 -0.2419728 -0.1962202 -0.2440769 0.08874210
## P11554_217 -0.1840496 -0.26787376 -0.3198303 -0.1813561 -0.3829422 0.04399071
## P11554_218 -0.2915297 -0.26121240 -0.5759900 -0.2869313 -0.1192221 -0.35275466
## P11554_225 -0.9389125 -0.77479754 -0.9324264 -0.9367352 -0.6039694 -0.56405649
## P11554_226 -0.8150359 -1.10248123 -0.7521130 -0.8295312 -0.6574796 -0.93819943
## P11554_227 -0.9178298 -0.92061846 -0.7676448 -0.9116850 -0.6032426 -0.85492408
## P11554_228 -1.4044524 -1.17752755 -1.1129111 -0.9353934 -1.3835633 -1.29380328
## P11554_229 -0.6845268 -0.92680555 -1.0730499 -1.2193252 -1.3584111 -1.46242494
## P11554_230 -1.4180303 -0.98343332 -1.1254472 -1.1846727 -1.2215076 -0.91228906
## AT3G49250 AT3G06030 AT5G43990 AT5G13960 AT2G38620 AT2G21800
## P11554_207 0.76182230 0.82102481 0.7567798 1.0043766 0.7091498 0.98031067
## P11554_208 1.00506220 1.01684596 0.6818722 1.3085413 1.2314364 0.86645912
## P11554_209 0.76986399 1.00721144 1.4158619 1.4788660 1.4824083 0.89846035
## P11554_210 -0.61754522 0.13697024 -0.7708602 -0.5948637 -0.4866701 0.11707096
## P11554_211 0.26859315 -0.20095345 -0.2919399 -0.3661511 -0.2831517 0.12366472
## P11554_212 -0.37966898 -0.16430412 -0.1086582 -0.2414945 -0.3545030 -0.10634112
## P11554_213 1.28148975 1.31455475 1.5458765 1.4390728 1.0683594 0.85496018
## P11554_214 1.75177795 1.41512011 1.7256013 1.2730129 1.5766051 1.64123137
## P11554_215 1.31526822 1.31921314 1.3918337 1.2866363 1.3268581 1.69749942
## P11554_216 0.08304583 -0.05486705 -0.3844021 -0.4534059 -0.1902658 -0.61084252
## P11554_217 0.16784242 -0.41115768 -0.1878223 -0.4221551 -0.2607280 -0.55744749
## P11554_218 -0.10292561 0.49781283 -0.3128184 -0.1337019 0.2311204 -0.23205276
## P11554_225 -1.34319574 -0.90703677 -1.2424826 -0.8574390 -0.9976361 -1.76136457
## P11554_226 -0.62472957 -0.82439278 -0.5601860 -0.7709018 -0.5765403 -1.16020415
## P11554_227 -0.37228891 -0.78627833 -0.3562295 -0.3838525 -0.5334090 -0.02943785
## P11554_228 -1.10646208 -1.48840682 -1.2494431 -1.3729869 -1.3054479 -0.73181780
## P11554_229 -1.21526705 -0.93162464 -1.1446612 -0.9757506 -1.3047874 -0.53051700
## P11554_230 -1.64268264 -1.75973165 -0.9083218 -1.2178030 -1.3327982 -1.45963154
## AT2G01905 AT2G07170 AT2G36200 AT2G32590
## P11554_207 1.710046799 1.16246877 0.789928494 0.9158040
## P11554_208 1.506037689 1.21521868 1.147157823 1.1134653
## P11554_209 1.267988288 1.21044060 1.240633443 1.2933929
## P11554_210 -0.329109796 -0.66107760 -0.023104453 -0.7870728
## P11554_211 -0.317900163 -0.12282299 -0.068006674 -0.1643060
## P11554_212 -0.005811059 0.10803380 -0.008155888 -0.2244563
## P11554_213 1.323202721 0.86065807 1.286910857 1.4311164
## P11554_214 0.827546245 1.47539009 1.451908875 1.1000030
## P11554_215 0.974138470 1.28567065 1.477508447 1.7474341
## P11554_216 -0.254739310 -0.12647254 -0.450342300 -0.3377033
## P11554_217 -0.976653536 0.05602871 -0.267145883 -0.5916351
## P11554_218 -0.323381468 0.23599004 -0.051833089 -0.1548873
## P11554_225 -1.281943965 -1.08364674 -1.305396182 -1.3558185
## P11554_226 -1.335965008 -1.05232203 -1.301268083 -0.9238693
## P11554_227 -0.609962188 -1.13010657 -1.127871684 -0.6470324
## P11554_228 -0.903000271 -1.31162882 -1.059346613 -1.4871688
## P11554_229 -0.462472609 -1.24453093 -0.846733569 -0.4577732
## P11554_230 -0.808020837 -0.87729120 -0.884843523 -0.4694927
##
## $`GO:0051726`$rowDendrogram
## 'dendrogram' with 2 branches and 140 members total, at height 3.94569
##
## $`GO:0051726`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0051726`$breaks
## [1] -2.75953113 -2.70434051 -2.64914989 -2.59395927 -2.53876864 -2.48357802
## [7] -2.42838740 -2.37319678 -2.31800615 -2.26281553 -2.20762491 -2.15243429
## [13] -2.09724366 -2.04205304 -1.98686242 -1.93167179 -1.87648117 -1.82129055
## [19] -1.76609993 -1.71090930 -1.65571868 -1.60052806 -1.54533744 -1.49014681
## [25] -1.43495619 -1.37976557 -1.32457494 -1.26938432 -1.21419370 -1.15900308
## [31] -1.10381245 -1.04862183 -0.99343121 -0.93824059 -0.88304996 -0.82785934
## [37] -0.77266872 -0.71747810 -0.66228747 -0.60709685 -0.55190623 -0.49671560
## [43] -0.44152498 -0.38633436 -0.33114374 -0.27595311 -0.22076249 -0.16557187
## [49] -0.11038125 -0.05519062 0.00000000 0.05519062 0.11038125 0.16557187
## [55] 0.22076249 0.27595311 0.33114374 0.38633436 0.44152498 0.49671560
## [61] 0.55190623 0.60709685 0.66228747 0.71747810 0.77266872 0.82785934
## [67] 0.88304996 0.93824059 0.99343121 1.04862183 1.10381245 1.15900308
## [73] 1.21419370 1.26938432 1.32457494 1.37976557 1.43495619 1.49014681
## [79] 1.54533744 1.60052806 1.65571868 1.71090930 1.76609993 1.82129055
## [85] 1.87648117 1.93167179 1.98686242 2.04205304 2.09724366 2.15243429
## [91] 2.20762491 2.26281553 2.31800615 2.37319678 2.42838740 2.48357802
## [97] 2.53876864 2.59395927 2.64914989 2.70434051 2.75953113
##
## $`GO:0051726`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0051726`$colorTable
## low high color
## 1 -2.75953113 -2.70434051 #0000FF
## 2 -2.70434051 -2.64914989 #0505FF
## 3 -2.64914989 -2.59395927 #0A0AFF
## 4 -2.59395927 -2.53876864 #0F0FFF
## 5 -2.53876864 -2.48357802 #1414FF
## 6 -2.48357802 -2.42838740 #1919FF
## 7 -2.42838740 -2.37319678 #1E1EFF
## 8 -2.37319678 -2.31800615 #2424FF
## 9 -2.31800615 -2.26281553 #2929FF
## 10 -2.26281553 -2.20762491 #2E2EFF
## 11 -2.20762491 -2.15243429 #3333FF
## 12 -2.15243429 -2.09724366 #3838FF
## 13 -2.09724366 -2.04205304 #3D3DFF
## 14 -2.04205304 -1.98686242 #4242FF
## 15 -1.98686242 -1.93167179 #4848FF
## 16 -1.93167179 -1.87648117 #4D4DFF
## 17 -1.87648117 -1.82129055 #5252FF
## 18 -1.82129055 -1.76609993 #5757FF
## 19 -1.76609993 -1.71090930 #5C5CFF
## 20 -1.71090930 -1.65571868 #6161FF
## 21 -1.65571868 -1.60052806 #6767FF
## 22 -1.60052806 -1.54533744 #6C6CFF
## 23 -1.54533744 -1.49014681 #7171FF
## 24 -1.49014681 -1.43495619 #7676FF
## 25 -1.43495619 -1.37976557 #7B7BFF
## 26 -1.37976557 -1.32457494 #8080FF
## 27 -1.32457494 -1.26938432 #8585FF
## 28 -1.26938432 -1.21419370 #8B8BFF
## 29 -1.21419370 -1.15900308 #9090FF
## 30 -1.15900308 -1.10381245 #9595FF
## 31 -1.10381245 -1.04862183 #9A9AFF
## 32 -1.04862183 -0.99343121 #9F9FFF
## 33 -0.99343121 -0.93824059 #A4A4FF
## 34 -0.93824059 -0.88304996 #AAAAFF
## 35 -0.88304996 -0.82785934 #AFAFFF
## 36 -0.82785934 -0.77266872 #B4B4FF
## 37 -0.77266872 -0.71747810 #B9B9FF
## 38 -0.71747810 -0.66228747 #BEBEFF
## 39 -0.66228747 -0.60709685 #C3C3FF
## 40 -0.60709685 -0.55190623 #C8C8FF
## 41 -0.55190623 -0.49671560 #CECEFF
## 42 -0.49671560 -0.44152498 #D3D3FF
## 43 -0.44152498 -0.38633436 #D8D8FF
## 44 -0.38633436 -0.33114374 #DDDDFF
## 45 -0.33114374 -0.27595311 #E2E2FF
## 46 -0.27595311 -0.22076249 #E7E7FF
## 47 -0.22076249 -0.16557187 #ECECFF
## 48 -0.16557187 -0.11038125 #F2F2FF
## 49 -0.11038125 -0.05519062 #F7F7FF
## 50 -0.05519062 0.00000000 #FCFCFF
## 51 0.00000000 0.05519062 #FFFCFC
## 52 0.05519062 0.11038125 #FFF7F7
## 53 0.11038125 0.16557187 #FFF2F2
## 54 0.16557187 0.22076249 #FFECEC
## 55 0.22076249 0.27595311 #FFE7E7
## 56 0.27595311 0.33114374 #FFE2E2
## 57 0.33114374 0.38633436 #FFDDDD
## 58 0.38633436 0.44152498 #FFD8D8
## 59 0.44152498 0.49671560 #FFD3D3
## 60 0.49671560 0.55190623 #FFCECE
## 61 0.55190623 0.60709685 #FFC8C8
## 62 0.60709685 0.66228747 #FFC3C3
## 63 0.66228747 0.71747810 #FFBEBE
## 64 0.71747810 0.77266872 #FFB9B9
## 65 0.77266872 0.82785934 #FFB4B4
## 66 0.82785934 0.88304996 #FFAFAF
## 67 0.88304996 0.93824059 #FFA9A9
## 68 0.93824059 0.99343121 #FFA4A4
## 69 0.99343121 1.04862183 #FF9F9F
## 70 1.04862183 1.10381245 #FF9A9A
## 71 1.10381245 1.15900308 #FF9595
## 72 1.15900308 1.21419370 #FF9090
## 73 1.21419370 1.26938432 #FF8B8B
## 74 1.26938432 1.32457494 #FF8585
## 75 1.32457494 1.37976557 #FF8080
## 76 1.37976557 1.43495619 #FF7B7B
## 77 1.43495619 1.49014681 #FF7676
## 78 1.49014681 1.54533744 #FF7171
## 79 1.54533744 1.60052806 #FF6C6C
## 80 1.60052806 1.65571868 #FF6767
## 81 1.65571868 1.71090930 #FF6161
## 82 1.71090930 1.76609993 #FF5C5C
## 83 1.76609993 1.82129055 #FF5757
## 84 1.82129055 1.87648117 #FF5252
## 85 1.87648117 1.93167179 #FF4D4D
## 86 1.93167179 1.98686242 #FF4848
## 87 1.98686242 2.04205304 #FF4242
## 88 2.04205304 2.09724366 #FF3D3D
## 89 2.09724366 2.15243429 #FF3838
## 90 2.15243429 2.20762491 #FF3333
## 91 2.20762491 2.26281553 #FF2E2E
## 92 2.26281553 2.31800615 #FF2929
## 93 2.31800615 2.37319678 #FF2424
## 94 2.37319678 2.42838740 #FF1E1E
## 95 2.42838740 2.48357802 #FF1919
## 96 2.48357802 2.53876864 #FF1414
## 97 2.53876864 2.59395927 #FF0F0F
## 98 2.59395927 2.64914989 #FF0A0A
## 99 2.64914989 2.70434051 #FF0505
## 100 2.70434051 2.75953113 #FF0000
##
## $`GO:0051726`$layout
## $`GO:0051726`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0051726`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0051726`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0009825`
## $`GO:0009825`$rowInd
## [1] 32 15 16 6 7 77 63 29 12 54 49 34 44 80 41 75 27 73 18 17 64 82 58 57 51
## [26] 65 61 13 28 59 81 38 74 72 76 37 71 78 43 3 46 83 42 5 52 22 10 36 48 24
## [51] 39 4 56 19 31 8 79 30 60 50 2 1 9 21 40 35 14 11 25 68 23 62 33 70 47
## [76] 45 26 67 53 66 55 20 69
##
## $`GO:0009825`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0009825`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0009825`$carpet
## AT2G20190 AT1G49040 AT1G58250 AT1G05850 AT1G10670
## P11554_207 -2.28218178 -1.4409725 -2.4283887 -1.43870549 -1.812601332
## P11554_208 -0.49514816 -0.4306467 0.7954388 -1.01068274 -1.076116866
## P11554_209 -0.56289907 0.7294349 0.8717575 -0.59211612 -0.612203857
## P11554_210 -0.87674593 -1.7465943 -0.7097829 -1.16912118 -0.508031951
## P11554_211 -0.85818751 -1.0136955 -1.4495324 -1.12533528 -0.531376678
## P11554_212 0.75521264 0.3299654 1.3607988 -0.85262580 -0.367493015
## P11554_213 -0.50789442 -0.1297716 -0.9272567 0.02438850 -0.716805151
## P11554_214 1.72630595 0.2392332 0.6829561 -0.07024538 -0.689297913
## P11554_215 1.00658737 -0.3815767 -0.7624221 -0.47341541 -0.701274708
## P11554_216 -0.33370851 -0.7128830 -0.4128755 0.00484085 0.006800093
## P11554_217 -0.24122932 0.5800763 1.3463368 -0.06538447 -0.047092829
## P11554_218 0.02664750 -0.7173010 -0.1192366 0.09336496 -0.018405471
## P11554_225 0.83491211 0.9149761 0.4814970 0.88418254 1.503063989
## P11554_226 1.16550623 1.5885562 0.5813550 1.89686568 1.491770599
## P11554_227 1.45674544 2.0338360 -0.2427777 1.82209087 1.848939835
## P11554_228 -0.73523928 -0.4733795 -0.2192989 0.01742714 0.202039977
## P11554_229 -0.11441205 0.8252470 0.5087664 1.29608567 1.119569667
## P11554_230 0.03572879 -0.1945045 0.6426650 0.75838566 0.908515611
## AT5G49720 AT5G01090 AT2G02130 AT1G23080 AT4G18710
## P11554_207 -0.6823674 -0.09015202 0.01713252 0.674748731 -1.216274915
## P11554_208 -0.9047459 0.32322628 0.05076319 0.426319350 -1.290426853
## P11554_209 -0.5661417 -0.32499450 -0.03928734 -0.691380173 -0.866838218
## P11554_210 -0.5465515 -1.02375119 -0.90925179 -0.012722497 0.834236455
## P11554_211 -0.5111637 -1.31942551 -0.93520142 -0.351838299 0.848678964
## P11554_212 -0.5312359 -0.55189534 -1.05071576 -0.597150415 0.849272907
## P11554_213 -0.5935653 -0.58046284 -0.37558268 -0.087036552 -1.239855103
## P11554_214 -0.7545226 -0.31657447 -0.34213695 -0.028887226 -1.606594544
## P11554_215 -0.7781193 -0.68043211 -0.43407410 -1.810929332 -1.364349410
## P11554_216 -0.6791795 -1.12356043 -1.13376506 0.192799452 0.429513460
## P11554_217 -0.5127397 -0.55572252 -1.14553558 0.052498066 0.192003268
## P11554_218 -0.5859705 -0.84741573 -1.18227594 0.001673925 0.613667344
## P11554_225 1.4951288 2.22686864 1.45984387 1.473101173 -0.002413995
## P11554_226 1.9789708 0.97273467 1.53401293 1.843796176 0.158985418
## P11554_227 2.0748340 1.70831161 1.53476641 1.707439114 0.165316518
## P11554_228 0.5691320 0.81107869 0.97305724 -0.588426362 0.853113798
## P11554_229 0.6930740 0.88103117 0.94000984 -0.463023393 1.564313074
## P11554_230 0.8351637 0.49113559 1.03824062 -1.740981738 1.077651833
## AT4G01710 AT2G35110 AT3G27000 AT5G64330 AT3G23050 AT5G28646
## P11554_207 -1.02457741 -1.12766340 -0.4279558 -0.74184868 -0.6671507 0.8393205
## P11554_208 -1.92764901 -0.92546091 -0.7990905 -0.42771097 -0.4122325 -1.1414701
## P11554_209 -0.31526634 -0.16136815 -0.9757085 -0.33287195 -0.5860213 -1.1414701
## P11554_210 1.19611385 1.16222671 0.1944211 0.29459574 0.5106285 1.1028001
## P11554_211 0.07998796 0.71551624 0.1515717 0.49176148 0.6011115 -1.1414701
## P11554_212 0.57737316 1.75834141 0.4177154 1.10910376 1.1684395 0.9238749
## P11554_213 -1.11210833 -1.88602659 -1.8489465 -1.60360225 -1.5226191 -1.1414701
## P11554_214 -0.87667361 -1.48077718 -1.0259444 -1.54885083 -1.0109060 0.3102521
## P11554_215 -1.61398917 -1.53036406 -1.5857696 -1.53866426 -2.0454680 -1.1414701
## P11554_216 0.51321881 0.19919032 0.1132091 -1.11962689 -0.6420635 0.3412774
## P11554_217 -0.07158179 0.39682708 0.1650685 -0.09277786 -0.4475978 -1.1414701
## P11554_218 0.48985680 0.34563823 0.2526989 -0.17602983 -0.4689222 0.2386424
## P11554_225 -0.39618910 0.36730541 0.4513085 0.98688077 0.4232849 1.4489162
## P11554_226 0.86065584 0.37626015 0.3950230 1.23913997 0.6429209 -1.1414701
## P11554_227 0.27863492 0.61785153 1.3064055 1.42560064 1.0390648 1.4215655
## P11554_228 1.26892759 -0.04805804 0.8403740 0.51737988 0.9715217 0.2214165
## P11554_229 0.53112965 0.41341391 2.2617883 0.70771404 1.4351375 0.6544848
## P11554_230 1.54213619 0.80714732 0.1138313 0.80980725 1.0108719 0.4877404
## AT1G80350 AT5G19530 AT1G69490 AT1G68530 AT5G05170
## P11554_207 -0.9210143 -0.2357023 -0.933121099 -1.2773911296 -1.97709478
## P11554_208 0.4173404 -0.2357023 -0.872664302 -1.1411272076 -1.62409129
## P11554_209 0.2060042 -0.2357023 -0.724020081 -1.2175560391 -1.34054902
## P11554_210 2.4492075 4.0069384 -0.311045068 -0.2245136358 0.31199408
## P11554_211 -0.6620706 -0.2357023 -0.130922974 -0.0008749247 -0.03145578
## P11554_212 -0.1809265 -0.2357023 -0.108150571 -0.0421397731 0.33925289
## P11554_213 -1.3557475 -0.2357023 -1.397445347 -1.0223561293 -0.57201339
## P11554_214 -1.1460196 -0.2357023 -0.878534598 -1.3009825678 -0.57303961
## P11554_215 0.5263613 -0.2357023 -0.941779697 -0.3481235187 -0.51729484
## P11554_216 0.1811567 -0.2357023 -0.008539624 1.0051780263 1.02016662
## P11554_217 -1.4076465 -0.2357023 0.186478653 0.8429466639 1.69703185
## P11554_218 0.5963907 -0.2357023 0.355065256 0.8449938383 1.60679581
## P11554_225 -0.8288288 -0.2357023 -0.085921076 0.0059472215 -0.22171608
## P11554_226 -0.5745994 -0.2357023 0.216734200 -0.3915162970 0.26960675
## P11554_227 1.4029087 -0.2357023 0.003104770 -0.2131078070 0.13047404
## P11554_228 0.1568745 -0.2357023 1.945053741 1.7929434057 0.25388050
## P11554_229 0.5127832 -0.2357023 1.445622511 1.0179811837 0.44091998
## P11554_230 0.6278260 -0.2357023 2.240085306 1.6696986903 0.78713228
## AT5G64740 AT4G32410 AT4G25570 AT4G03190 AT5G05690
## P11554_207 -2.014962e+00 -1.96913613 -0.84883168 -1.54199648 -0.5599841
## P11554_208 -1.359551e+00 -1.79301975 -0.71936723 -0.98771680 -0.4097569
## P11554_209 -1.837182e+00 -1.81509513 0.05851049 -0.75767772 -0.1061118
## P11554_210 -8.596158e-02 -0.20907940 0.13894337 1.05104985 0.9842324
## P11554_211 -3.567546e-05 -0.07905556 -0.02295902 1.26981383 0.6501148
## P11554_212 1.664214e-01 0.12949894 0.61441819 0.87812034 0.6044131
## P11554_213 -7.127469e-01 -0.33188830 -1.04066882 -0.97365817 -1.2572266
## P11554_214 -3.638990e-01 -0.31150590 -0.92656912 -0.24427344 -1.2331532
## P11554_215 -6.055002e-01 -0.50231428 -0.38573771 -0.99637785 -1.3686288
## P11554_216 1.153162e+00 0.55469477 1.44068492 1.56129308 0.9256641
## P11554_217 1.117372e+00 0.84259192 1.48855931 1.29446184 1.4520231
## P11554_218 4.630431e-01 0.76294832 2.24351207 1.13019023 1.1631404
## P11554_225 9.203314e-01 0.21825013 -1.63464700 -1.06269614 -1.5411179
## P11554_226 4.045431e-01 0.71543460 -0.41720025 -0.25094384 -0.3253863
## P11554_227 4.638969e-01 0.51031723 -0.14117964 -0.66939864 -1.1123328
## P11554_228 1.328551e+00 0.96165804 -0.62960716 0.02748101 0.8853658
## P11554_229 1.902588e-02 0.98304785 0.82572558 0.64365109 0.9212474
## P11554_230 9.434914e-01 1.33265267 -0.04358631 -0.37132218 0.3274971
## AT4G38430 AT1G28440 AT2G01420 AT4G33000 AT5G64340
## P11554_207 -1.558857610 0.97746540 0.15236853 0.6057781 -0.276784304
## P11554_208 -0.643273626 -0.35144929 -0.07299311 0.3065574 -1.443748422
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## P11554_210 -0.014313620 0.70134344 0.88981697 0.6221513 1.391899234
## P11554_211 0.281295807 1.03980494 1.80615453 0.9722309 1.901066276
## P11554_212 0.610415792 0.91091508 0.76524454 0.8296339 1.429554727
## P11554_213 -1.056307610 -0.05974311 -0.78106972 -0.3150898 0.422574440
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## P11554_216 1.098578204 1.26968910 1.31493490 0.9965131 0.905710797
## P11554_217 1.801970383 0.79678088 1.17415993 0.6173667 0.243995208
## P11554_218 1.032837526 0.70050691 0.48384647 1.3481437 -0.006127085
## P11554_225 0.088601558 -0.37559356 0.59175771 0.7853968 0.723668531
## P11554_226 0.007914576 -0.64782905 0.02222867 0.0725274 -0.478690853
## P11554_227 0.677634697 -1.73288865 -0.10847839 -0.7358714 -0.938841224
## P11554_228 0.058239274 0.25165721 -0.86031424 0.6369099 0.197950857
## P11554_229 0.973297431 -1.65560721 -1.84422703 -0.7171010 -0.742792035
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## AT3G16370 AT5G25810 AT5G17690 AT5G35360 AT2G39900 AT5G16390
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## P11554_208 -0.9104516 -0.6142808 0.08629735 0.6962365 0.7470900 0.57834057
## P11554_209 1.4069450 0.7157153 0.81795916 0.7571425 1.1293947 0.96426130
## P11554_210 -0.9104516 0.5860934 -0.23315873 -0.5399454 -0.3168960 -0.58414928
## P11554_211 0.3665829 -1.1543691 0.13917410 -0.8783955 -0.7568318 -0.66281860
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## P11554_213 -0.9104516 1.3201254 0.85257460 1.1982068 1.6424281 1.73218276
## P11554_214 1.0961653 1.3689348 0.15463817 2.2680933 1.6328567 1.40444278
## P11554_215 -0.9104516 -1.2427972 -2.47428659 1.5221335 1.0961000 1.73928315
## P11554_216 0.5389335 -0.1314794 0.01090603 -0.4135534 -0.1881365 0.17576184
## P11554_217 1.9043392 -0.5299937 0.89815655 0.1282068 0.3099101 0.15542037
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## P11554_225 0.8803470 0.3059898 1.38816874 -0.3186570 -0.2664552 -0.30254969
## P11554_226 -0.9104516 -0.5111195 -0.03814341 0.1939218 -0.6535948 -0.09192852
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## P11554_229 -0.9104516 -2.0426386 -0.46475893 -0.5785580 -1.1432237 -1.25644653
## P11554_230 -0.9104516 -0.9543731 -0.29635725 -1.0391277 -1.0977185 -1.04691802
## AT5G55540 AT3G26520 AT1G04040 AT3G46550 AT5G65700
## P11554_207 0.45842811 0.23014574 0.69868343 0.89128591 0.545229250
## P11554_208 1.34242890 0.63017688 0.65342847 0.27778323 0.543852156
## P11554_209 0.83559809 0.90574984 0.67558289 0.07905788 -0.061085844
## P11554_210 -1.52150643 -1.07504471 -0.90059661 0.11268968 -0.387254030
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## P11554_213 1.50301863 1.68684336 1.38350656 1.44718296 1.664490404
## P11554_214 1.70967763 1.64047544 1.50421226 1.49474659 1.805586283
## P11554_215 1.32582354 0.82109642 1.57236454 1.16522141 0.742680387
## P11554_216 0.10373725 0.60115677 0.19373283 0.97871702 0.178367913
## P11554_217 -0.02560587 0.14242723 0.27976667 0.70251301 0.006242576
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## P11554_226 -0.09127750 -0.51770569 -0.05562969 -0.77513617 0.208305996
## P11554_227 -0.01891151 -0.06849779 0.03523223 -0.65080881 0.197013282
## P11554_228 -1.06594390 -1.41910723 -1.46594192 -0.94474116 -0.758595177
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## P11554_230 -0.82758167 -1.80427044 -1.59017531 -1.99052258 -2.014104540
## AT3G25500 AT1G04680 AT4G12420 AT1G75680 AT1G20330
## P11554_207 0.103237632 0.1305210 0.4206323 0.001797876 -0.037613419
## P11554_208 -0.021433789 0.1393429 0.4059979 -0.053148160 0.072492370
## P11554_209 -0.069116811 0.1162978 0.3106473 0.433190878 -0.001877165
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## P11554_213 1.551500379 1.6795027 1.6442348 1.769265442 1.700101288
## P11554_214 1.385175987 1.5740844 1.6537383 1.850056452 1.283928358
## P11554_215 1.652816898 1.7061328 1.7463457 1.677400362 1.697073816
## P11554_216 0.869012687 0.6914776 0.5284163 0.380977956 0.933407517
## P11554_217 0.930364392 0.8112199 0.4965759 0.361631947 0.685152675
## P11554_218 0.512213085 0.8126033 0.4767656 0.606641794 0.983287363
## P11554_225 -0.657042935 -0.9888344 -0.9413676 -0.477236839 -0.492834676
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## P11554_227 -1.030200670 -0.9145951 -0.9205760 -0.779850234 -0.929366085
## P11554_228 -1.037087097 -0.9693095 -1.1775179 -1.397980228 -1.218674281
## P11554_229 -1.540287288 -1.1007868 -1.0847362 -0.912493743 -1.032602120
## P11554_230 -1.494391624 -1.1129963 -1.2854785 -1.482138331 -1.550721353
## AT2G38120 AT3G54920 AT1G75780 AT3G18780 AT1G04430
## P11554_207 0.0394464878 -0.1002383 0.7535133 0.34721068 0.09369149
## P11554_208 0.0008088777 0.1686417 0.7876900 0.90393924 0.09799811
## P11554_209 0.4156624175 -0.0241720 0.8299920 0.92547420 0.12477088
## P11554_210 -0.6188198959 -0.4622545 -0.6759297 -0.19105964 -0.79691349
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## P11554_212 -0.2351539872 -0.3677630 -0.2992172 -0.28823046 -0.47559532
## P11554_213 1.3588589121 1.4829512 1.4199078 1.27756931 1.83665848
## P11554_214 1.2629697932 1.4118994 1.3594669 1.38187080 1.69311865
## P11554_215 1.5599464210 1.5656610 1.1466363 1.51976546 1.99377540
## P11554_216 1.0086633279 0.9786680 0.7069129 0.25903341 0.06882908
## P11554_217 0.8592823538 1.1127158 0.4538419 0.32756349 0.19793365
## P11554_218 1.0676436220 0.8966971 0.3200301 0.44152921 0.40304813
## P11554_225 -1.0326034154 -0.9039239 -1.0627790 -1.34915980 -0.38620006
## P11554_226 -0.7439106568 -0.7700348 -0.4875277 -0.73250745 -0.12425794
## P11554_227 -0.7591355400 -0.9281876 -0.3711048 -0.94271219 -0.11703539
## P11554_228 -1.7244602130 -1.5157847 -1.6827823 -1.87117389 -1.32676721
## P11554_229 -0.7472180405 -0.9327575 -0.9101244 -0.85690584 -1.22007714
## P11554_230 -1.3160351926 -1.1447635 -1.7789375 -1.17635286 -1.28466354
## AT4G22010 AT1G70370 AT2G06850 AT1G13180 AT5G60920
## P11554_207 -0.1004695 0.1321233190 -0.28418932 -0.32819847 -0.67194342
## P11554_208 -0.3557234 0.0463369751 -0.02655698 -0.13117949 -0.76416858
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## P11554_210 -0.5948613 -0.8219879616 -1.31683186 -1.93887820 -0.76678497
## P11554_211 -0.5364894 -0.5881166670 -1.25182637 -1.42291154 -0.87232119
## P11554_212 -0.5711944 -0.6473969795 -1.31223910 -1.23882381 -0.68294702
## P11554_213 1.9802822 2.0218741487 1.43012791 1.01662046 1.30515024
## P11554_214 1.9402287 2.0138477053 1.60786692 1.14425723 1.09195439
## P11554_215 2.0026420 2.0236322925 1.53054544 2.11697475 1.55173740
## P11554_216 0.3785924 -0.0134925836 0.87775225 0.66013620 0.18640108
## P11554_217 0.3836589 -0.0007030037 0.90492857 0.19445438 0.06438717
## P11554_218 0.3472979 0.1533455530 0.85858598 0.72196402 0.48496024
## P11554_225 -0.5436030 -0.5860777012 -0.12844153 -0.47124739 0.46897696
## P11554_226 -0.5975724 -0.4963712601 0.05377913 -0.74625648 1.54843541
## P11554_227 -0.5351365 -0.6304553438 -0.01169223 0.65750016 1.05026821
## P11554_228 -0.9048802 -0.8343048311 -0.92802097 -0.47670250 -1.38678177
## P11554_229 -0.8699981 -0.9510708155 -0.99679771 -0.19231427 -0.80752648
## P11554_230 -1.0725552 -0.8302752381 -0.83097726 0.50649880 -1.47257540
## AT2G03680 AT4G34490 AT4G02500 AT1G03060 AT1G01610
## P11554_207 -0.03054995 0.1576405 -0.42200558 -0.373849458 -0.33464569
## P11554_208 0.53077080 0.5046696 -0.17516191 -0.007727273 -0.30532881
## P11554_209 1.11361999 0.3029150 -0.30186229 -0.689497141 0.49463864
## P11554_210 -0.83760348 -1.4410397 -1.06517094 -1.313972982 -0.03463039
## P11554_211 -1.36049477 -1.4601673 -1.75731088 -0.017491051 0.17783810
## P11554_212 -0.86325799 -1.0189151 -1.52586382 0.318937269 -0.14233778
## P11554_213 0.77975799 1.2693461 1.43277002 -1.234734097 -0.43344970
## P11554_214 0.56061346 1.2528968 1.08768781 0.619754601 0.08675036
## P11554_215 0.56631863 1.3559358 1.03857551 2.089295842 1.19661033
## P11554_216 -0.17098674 -0.3813236 -0.58082434 1.159326467 1.68845265
## P11554_217 -0.85300731 -0.4497620 -0.65543088 2.131706252 1.81916667
## P11554_218 -0.48875702 -0.1477535 -0.40281928 0.105761537 1.29801207
## P11554_225 0.52481123 0.8761985 0.74712115 -0.845794862 -1.84699698
## P11554_226 1.61657790 1.0862091 1.94251131 -0.957614055 -1.32419917
## P11554_227 1.80662779 1.0057022 0.72669071 -0.239883943 -1.06588120
## P11554_228 -1.75601576 -1.2609505 -0.19703573 -0.829228451 -0.10002299
## P11554_229 -0.40122462 -0.6259879 0.03076861 0.012245535 -0.69780163
## P11554_230 -0.73720014 -1.0256140 0.07736055 0.072765810 -0.47617448
## AT1G20090 AT1G75500 AT3G19820 AT2G35620 AT1G31420
## P11554_207 -0.983719794 -0.3902587 -0.54533063 -0.55495962 -0.63914798
## P11554_208 -0.918627710 -0.2868709 -0.31151040 0.14223958 -0.45979071
## P11554_209 -0.659476038 -0.2257476 -0.01902099 -0.37271774 -0.25158051
## P11554_210 -0.737783294 -0.5722793 -0.21898309 -0.57288008 -0.17980932
## P11554_211 0.009207102 -0.7715492 -0.08166242 0.14354116 -0.09436904
## P11554_212 0.059048358 -0.4532669 -0.22749764 0.05080408 -0.35565893
## P11554_213 1.318783003 1.4466148 0.58341604 1.18474768 1.54754243
## P11554_214 0.953749615 1.4544411 0.65260557 1.26158757 1.03624783
## P11554_215 1.266885662 1.3546947 1.07389620 1.15230527 0.70991783
## P11554_216 1.535511254 1.3416080 1.47542973 1.17295103 1.76415529
## P11554_217 1.456091735 1.2437729 1.83873147 1.49467941 1.28186137
## P11554_218 1.303033001 1.0929334 1.54903489 1.03748104 0.61026981
## P11554_225 -0.696623841 -1.2169398 -1.03889363 -0.84517591 -0.19666369
## P11554_226 -1.000706175 -1.0947589 -0.62547497 -0.60963820 -0.12918129
## P11554_227 -0.470655839 -0.9605654 -0.45348122 -0.53251688 -0.49806389
## P11554_228 -0.607525813 -0.8580990 -1.68029178 -1.48131700 -0.60187145
## P11554_229 -0.792601888 -0.3876202 -0.68541741 -1.19259641 -1.54456132
## P11554_230 -1.034589339 -0.7161092 -1.28554971 -1.47853499 -1.99929644
## AT1G20340 AT1G75840 AT5G13140 AT1G75750 AT4G39400
## P11554_207 1.01644381 0.54694352 -1.26297727 -0.95375884 1.385782906
## P11554_208 1.45661734 0.45025982 -1.27697821 -0.51670471 1.131456424
## P11554_209 0.22632970 -0.75304842 -0.52706148 -1.02196971 0.958323074
## P11554_210 -0.05794997 0.29189740 -0.50095982 -0.65514389 -0.076478699
## P11554_211 -0.09428053 -0.72815192 -0.21136520 -0.76821814 0.310177409
## P11554_212 -0.38495847 -0.26485244 -1.01818255 -0.81158314 -0.167607977
## P11554_213 0.84235799 1.10655835 1.27879419 0.48207136 1.054076419
## P11554_214 0.72785802 1.05329683 0.53897804 0.58784168 1.788821503
## P11554_215 0.30960630 1.18271116 0.32249849 0.11469440 -0.091168748
## P11554_216 0.41275914 0.84567814 2.24534277 2.05027800 0.403506729
## P11554_217 1.03087469 1.16907449 0.28535322 1.77428864 -0.009908983
## P11554_218 1.41066395 0.99186040 0.87076374 1.74650183 -0.543731381
## P11554_225 -0.56947245 -0.84085844 -0.04046908 0.02415789 -0.184896670
## P11554_226 -1.34218368 -1.98862335 0.54930951 0.27570880 -0.976717812
## P11554_227 -1.26224848 -0.58047786 0.48550228 0.11929717 -1.286183995
## P11554_228 -1.73900921 0.06593904 -1.04337266 -0.70213291 -0.548636253
## P11554_229 -0.56446714 -0.95991485 0.74413081 -0.85172064 -1.771386981
## P11554_230 -1.41894101 -1.58829187 -1.43930677 -0.89360778 -1.375426965
## AT2G22230 AT5G16000 AT3G49670 AT3G28860 AT1G77690
## P11554_207 1.0627713 1.32218058 1.4360529 0.54681087 1.25858416
## P11554_208 1.3035155 1.15514663 1.0212062 1.80613819 1.29833018
## P11554_209 1.1822391 1.18460195 0.9937498 2.16661571 1.29806366
## P11554_210 -0.2938410 -0.50346485 -0.3790207 0.07153399 -0.08319365
## P11554_211 -0.6770948 -0.53808854 -0.3085628 -0.49101941 -0.44865092
## P11554_212 -0.6309863 -0.37373781 -0.5917863 -1.05085720 0.04604019
## P11554_213 1.2224555 1.47046117 1.5127321 0.71420168 1.41329883
## P11554_214 1.3060921 1.33880034 1.5467758 1.19823743 0.93459776
## P11554_215 1.3158271 1.01071823 1.0893604 0.54238190 0.91310351
## P11554_216 -0.2496589 0.01872454 -0.4058656 -0.25044487 -0.57331632
## P11554_217 -0.1034830 -0.18638494 0.1190370 -0.25845368 -1.38474177
## P11554_218 -0.2956307 -0.12433466 -0.6735481 -0.72762278 -0.20878277
## P11554_225 -0.5057470 -0.37063862 -0.5009542 -0.45836919 -0.46281390
## P11554_226 -0.1150234 -0.44738873 -0.8079379 -0.57264912 -0.35890205
## P11554_227 -0.1712178 -0.75997242 -0.2929350 -0.86536408 -0.57610251
## P11554_228 -1.7075093 -1.28621057 -1.0099797 -0.58891672 -0.70081258
## P11554_229 -1.1933839 -1.46148411 -1.2478727 -1.68900357 -2.15153189
## P11554_230 -1.4493246 -1.44892820 -1.5004512 -0.09321917 -0.21316992
## AT5G12250 AT4G16370 AT5G10480 AT4G20270 AT1G70940 AT5G15580
## P11554_207 1.01310448 1.3422224 1.5715760 1.5179526 1.0366200 1.02178742
## P11554_208 1.07728782 1.6146736 1.3639700 1.6981218 0.6948856 0.78256022
## P11554_209 1.74123425 1.9323134 1.0121945 1.3365347 0.6959209 -1.19950752
## P11554_210 -0.22340226 -0.8496640 -1.0062667 -0.1817974 -0.6718035 -1.19950752
## P11554_211 -0.05105366 -0.3137256 -0.8318559 -0.4130531 -0.6620231 0.49221522
## P11554_212 -0.15911724 -0.4179660 -1.5981943 -0.0108936 -0.6008609 0.13800552
## P11554_213 0.62819604 -0.1750249 1.0763069 0.4164654 0.5871451 2.03796579
## P11554_214 0.94442155 0.3432319 0.3090903 0.2807110 0.3735167 0.12988330
## P11554_215 0.34820451 0.1672251 1.0738117 -0.5662655 -0.1316799 0.16387542
## P11554_216 -0.23399446 -0.3770950 -0.3728101 -1.4086533 -1.1124177 -1.19950752
## P11554_217 -0.51877346 -0.7531351 -0.6060035 -1.5492392 -1.0332450 0.11941155
## P11554_218 -0.14546970 -0.8167276 -0.5070895 -1.1714298 -1.4056628 -1.19950752
## P11554_225 -0.22207016 0.2208150 0.4120355 1.0140866 1.6854588 1.17259628
## P11554_226 0.45539693 1.0219985 0.5006293 0.6478689 1.3605829 0.18013072
## P11554_227 0.40784419 0.7569491 0.6556301 0.6129272 1.4339803 -1.19950752
## P11554_228 -2.43063000 -1.3176311 -0.8887407 -0.6231104 -0.1813889 0.04853354
## P11554_229 -1.03457418 -0.9909587 -1.4240676 -0.8067912 -1.0761732 -1.19950752
## P11554_230 -1.59660466 -1.3875010 -0.7402163 -0.7934348 -0.9928553 0.91008012
##
## $`GO:0009825`$rowDendrogram
## 'dendrogram' with 2 branches and 83 members total, at height 3.456072
##
## $`GO:0009825`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0009825`$breaks
## [1] -4.00693843 -3.92679966 -3.84666089 -3.76652212 -3.68638335 -3.60624458
## [7] -3.52610582 -3.44596705 -3.36582828 -3.28568951 -3.20555074 -3.12541197
## [13] -3.04527320 -2.96513444 -2.88499567 -2.80485690 -2.72471813 -2.64457936
## [19] -2.56444059 -2.48430182 -2.40416306 -2.32402429 -2.24388552 -2.16374675
## [25] -2.08360798 -2.00346921 -1.92333044 -1.84319168 -1.76305291 -1.68291414
## [31] -1.60277537 -1.52263660 -1.44249783 -1.36235907 -1.28222030 -1.20208153
## [37] -1.12194276 -1.04180399 -0.96166522 -0.88152645 -0.80138769 -0.72124892
## [43] -0.64111015 -0.56097138 -0.48083261 -0.40069384 -0.32055507 -0.24041631
## [49] -0.16027754 -0.08013877 0.00000000 0.08013877 0.16027754 0.24041631
## [55] 0.32055507 0.40069384 0.48083261 0.56097138 0.64111015 0.72124892
## [61] 0.80138769 0.88152645 0.96166522 1.04180399 1.12194276 1.20208153
## [67] 1.28222030 1.36235907 1.44249783 1.52263660 1.60277537 1.68291414
## [73] 1.76305291 1.84319168 1.92333044 2.00346921 2.08360798 2.16374675
## [79] 2.24388552 2.32402429 2.40416306 2.48430182 2.56444059 2.64457936
## [85] 2.72471813 2.80485690 2.88499567 2.96513444 3.04527320 3.12541197
## [91] 3.20555074 3.28568951 3.36582828 3.44596705 3.52610582 3.60624458
## [97] 3.68638335 3.76652212 3.84666089 3.92679966 4.00693843
##
## $`GO:0009825`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0009825`$colorTable
## low high color
## 1 -4.00693843 -3.92679966 #0000FF
## 2 -3.92679966 -3.84666089 #0505FF
## 3 -3.84666089 -3.76652212 #0A0AFF
## 4 -3.76652212 -3.68638335 #0F0FFF
## 5 -3.68638335 -3.60624458 #1414FF
## 6 -3.60624458 -3.52610582 #1919FF
## 7 -3.52610582 -3.44596705 #1E1EFF
## 8 -3.44596705 -3.36582828 #2424FF
## 9 -3.36582828 -3.28568951 #2929FF
## 10 -3.28568951 -3.20555074 #2E2EFF
## 11 -3.20555074 -3.12541197 #3333FF
## 12 -3.12541197 -3.04527320 #3838FF
## 13 -3.04527320 -2.96513444 #3D3DFF
## 14 -2.96513444 -2.88499567 #4242FF
## 15 -2.88499567 -2.80485690 #4848FF
## 16 -2.80485690 -2.72471813 #4D4DFF
## 17 -2.72471813 -2.64457936 #5252FF
## 18 -2.64457936 -2.56444059 #5757FF
## 19 -2.56444059 -2.48430182 #5C5CFF
## 20 -2.48430182 -2.40416306 #6161FF
## 21 -2.40416306 -2.32402429 #6767FF
## 22 -2.32402429 -2.24388552 #6C6CFF
## 23 -2.24388552 -2.16374675 #7171FF
## 24 -2.16374675 -2.08360798 #7676FF
## 25 -2.08360798 -2.00346921 #7B7BFF
## 26 -2.00346921 -1.92333044 #8080FF
## 27 -1.92333044 -1.84319168 #8585FF
## 28 -1.84319168 -1.76305291 #8B8BFF
## 29 -1.76305291 -1.68291414 #9090FF
## 30 -1.68291414 -1.60277537 #9595FF
## 31 -1.60277537 -1.52263660 #9A9AFF
## 32 -1.52263660 -1.44249783 #9F9FFF
## 33 -1.44249783 -1.36235907 #A4A4FF
## 34 -1.36235907 -1.28222030 #AAAAFF
## 35 -1.28222030 -1.20208153 #AFAFFF
## 36 -1.20208153 -1.12194276 #B4B4FF
## 37 -1.12194276 -1.04180399 #B9B9FF
## 38 -1.04180399 -0.96166522 #BEBEFF
## 39 -0.96166522 -0.88152645 #C3C3FF
## 40 -0.88152645 -0.80138769 #C8C8FF
## 41 -0.80138769 -0.72124892 #CECEFF
## 42 -0.72124892 -0.64111015 #D3D3FF
## 43 -0.64111015 -0.56097138 #D8D8FF
## 44 -0.56097138 -0.48083261 #DDDDFF
## 45 -0.48083261 -0.40069384 #E2E2FF
## 46 -0.40069384 -0.32055507 #E7E7FF
## 47 -0.32055507 -0.24041631 #ECECFF
## 48 -0.24041631 -0.16027754 #F2F2FF
## 49 -0.16027754 -0.08013877 #F7F7FF
## 50 -0.08013877 0.00000000 #FCFCFF
## 51 0.00000000 0.08013877 #FFFCFC
## 52 0.08013877 0.16027754 #FFF7F7
## 53 0.16027754 0.24041631 #FFF2F2
## 54 0.24041631 0.32055507 #FFECEC
## 55 0.32055507 0.40069384 #FFE7E7
## 56 0.40069384 0.48083261 #FFE2E2
## 57 0.48083261 0.56097138 #FFDDDD
## 58 0.56097138 0.64111015 #FFD8D8
## 59 0.64111015 0.72124892 #FFD3D3
## 60 0.72124892 0.80138769 #FFCECE
## 61 0.80138769 0.88152645 #FFC8C8
## 62 0.88152645 0.96166522 #FFC3C3
## 63 0.96166522 1.04180399 #FFBEBE
## 64 1.04180399 1.12194276 #FFB9B9
## 65 1.12194276 1.20208153 #FFB4B4
## 66 1.20208153 1.28222030 #FFAFAF
## 67 1.28222030 1.36235907 #FFA9A9
## 68 1.36235907 1.44249783 #FFA4A4
## 69 1.44249783 1.52263660 #FF9F9F
## 70 1.52263660 1.60277537 #FF9A9A
## 71 1.60277537 1.68291414 #FF9595
## 72 1.68291414 1.76305291 #FF9090
## 73 1.76305291 1.84319168 #FF8B8B
## 74 1.84319168 1.92333044 #FF8585
## 75 1.92333044 2.00346921 #FF8080
## 76 2.00346921 2.08360798 #FF7B7B
## 77 2.08360798 2.16374675 #FF7676
## 78 2.16374675 2.24388552 #FF7171
## 79 2.24388552 2.32402429 #FF6C6C
## 80 2.32402429 2.40416306 #FF6767
## 81 2.40416306 2.48430182 #FF6161
## 82 2.48430182 2.56444059 #FF5C5C
## 83 2.56444059 2.64457936 #FF5757
## 84 2.64457936 2.72471813 #FF5252
## 85 2.72471813 2.80485690 #FF4D4D
## 86 2.80485690 2.88499567 #FF4848
## 87 2.88499567 2.96513444 #FF4242
## 88 2.96513444 3.04527320 #FF3D3D
## 89 3.04527320 3.12541197 #FF3838
## 90 3.12541197 3.20555074 #FF3333
## 91 3.20555074 3.28568951 #FF2E2E
## 92 3.28568951 3.36582828 #FF2929
## 93 3.36582828 3.44596705 #FF2424
## 94 3.44596705 3.52610582 #FF1E1E
## 95 3.52610582 3.60624458 #FF1919
## 96 3.60624458 3.68638335 #FF1414
## 97 3.68638335 3.76652212 #FF0F0F
## 98 3.76652212 3.84666089 #FF0A0A
## 99 3.84666089 3.92679966 #FF0505
## 100 3.92679966 4.00693843 #FF0000
##
## $`GO:0009825`$layout
## $`GO:0009825`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0009825`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0009825`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0048519`
## $`GO:0048519`$rowInd
## [1] 8 31 5 35 36 12 15 33 26 28 6 13 10 7 30 2 22 25 39 4 21 24 43 41 20
## [26] 18 42 38 19 27 16 37 3 44 1 17 32 46 9 14 23 11 40 29 34 45
##
## $`GO:0048519`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0048519`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0048519`$carpet
## AT1G52150 AT4G36260 AT1G19850 AT5G13300 AT5G25475
## P11554_207 0.156572852 -0.29479406 -1.92210941 -1.932065495 -1.6756594
## P11554_208 0.676954544 -0.57527208 -1.36846994 -1.068069619 -1.3156358
## P11554_209 0.008466485 -0.58433351 -0.73215680 -1.064417090 -1.5989665
## P11554_210 0.783778518 -0.08474480 0.78571471 -0.020603039 0.9298602
## P11554_211 -0.602879193 0.06675601 0.53335362 0.361416256 -0.0113235
## P11554_212 -0.178865691 -0.11015446 0.71795770 1.330457447 0.6815380
## P11554_213 -0.499098477 -1.56203200 0.26614883 -0.540481640 -0.1574369
## P11554_214 -0.161025108 -1.26404345 -0.07461912 -1.053435751 -1.4671597
## P11554_215 -1.690160563 -1.21625579 -0.66321046 -1.283056017 -0.5528083
## P11554_216 0.723860643 0.06939648 -0.43212757 0.301350938 0.9437296
## P11554_217 -0.992758887 0.14902350 0.10041533 1.878222099 0.6885873
## P11554_218 -0.201427481 0.46787861 -0.04367846 0.314316015 1.5370129
## P11554_225 -1.199809979 -0.78257035 -0.45574361 0.176382530 -0.6195375
## P11554_226 -1.257812386 0.29630969 -0.71027621 0.099686874 0.1498166
## P11554_227 -0.144536552 0.07636573 -0.70199737 1.079499443 0.6026779
## P11554_228 0.867014126 2.15570585 1.32800851 -0.007849787 0.5309910
## P11554_229 2.123158085 1.55171551 1.45399474 0.490880804 1.1273434
## P11554_230 1.588569062 1.64104914 1.91879550 0.937766033 0.2069706
## AT1G70510 AT1G79420 AT5G02030 AT3G43920 AT4G08150
## P11554_207 -1.01131630 -1.1028652 -0.6329378 -1.64727307 0.37590680
## P11554_208 -1.56447815 -1.1917885 -0.6179165 -0.91117855 -0.04447810
## P11554_209 -1.33033933 -1.0412391 -0.3524780 -0.42900811 -1.03632017
## P11554_210 0.88088994 0.1544668 1.1595349 0.61625960 1.11318062
## P11554_211 0.46887833 0.7710753 1.3132091 1.07774021 1.13983336
## P11554_212 1.62836124 0.4252904 1.1799659 1.04526891 1.96051502
## P11554_213 -1.01291010 -1.7736890 -1.8140522 -1.66881669 -1.31856193
## P11554_214 -0.74597588 -1.0421616 -1.6393306 -0.83540882 -1.11833320
## P11554_215 -1.53663203 -0.9829379 -1.4745319 -1.38626714 -1.91834763
## P11554_216 0.19304709 1.4363963 0.8264781 0.86854066 0.04212180
## P11554_217 0.32637763 0.8893524 0.7574347 1.58115735 -0.63823425
## P11554_218 1.36583023 0.7987895 0.5978811 0.90555754 -0.04605341
## P11554_225 -0.46303259 -0.1058179 -0.2084781 -0.12680717 -0.36267578
## P11554_226 0.58362602 -0.4813264 -0.4786688 -0.17036943 0.40792919
## P11554_227 0.03432441 0.1809118 -0.5550081 -0.30558078 -0.42609481
## P11554_228 0.64035419 1.2716288 0.5059021 -0.02024755 -0.04738538
## P11554_229 0.80902353 1.2762117 0.7481412 0.57803997 0.98078032
## P11554_230 0.73397176 0.5177025 0.6848550 0.82839307 0.93621757
## AT1G30330 AT1G73590 AT1G60860 AT1G48410 AT4G32551
## P11554_207 0.37934066 -0.1151538 -1.76418508 -1.52185850 -0.24586246
## P11554_208 -0.92726383 -0.2941705 1.04476694 0.05451137 -0.02343463
## P11554_209 -0.29809229 -0.3176070 -1.04317608 0.29427536 1.24411664
## P11554_210 0.13255580 -0.2657448 -1.52609755 -1.20210992 -1.44750996
## P11554_211 0.18115603 -0.3123709 -0.80043708 -1.01390535 -0.96563300
## P11554_212 -0.55767153 -0.3816624 0.04036054 -0.17301048 -1.40266329
## P11554_213 -0.10539620 -0.5371149 0.44329222 0.48140777 0.55744855
## P11554_214 0.86483836 -0.6531772 0.24602003 0.93994463 -0.33049464
## P11554_215 1.04995918 -1.0692602 -0.51819749 0.46290840 1.41713729
## P11554_216 0.15032905 -1.0119873 -1.12831809 0.73776929 0.60384180
## P11554_217 -0.91906143 -1.1585317 -0.63820830 1.72800670 -0.35985219
## P11554_218 -2.60235619 -1.3913922 -0.23912672 1.12843318 0.75311016
## P11554_225 1.23596415 1.7004744 0.65532742 -1.93815311 -1.04945055
## P11554_226 1.19254147 1.5557086 1.44164004 -0.82091856 1.10591582
## P11554_227 0.80507326 1.5832300 1.41305039 0.47505566 0.96265526
## P11554_228 0.75969663 1.1805458 0.74612759 -0.70839668 -1.78357653
## P11554_229 0.02562416 0.6931540 0.60332578 0.20531390 0.41395223
## P11554_230 -1.36723729 0.7950598 1.02383544 0.87072635 0.55029948
## AT1G05470 AT3G06220 AT3G28730 AT5G57130 AT1G19100
## P11554_207 -0.55064565 0.93786779 -0.13054870 1.4512796 0.85285717
## P11554_208 1.72393185 0.08097672 0.19426429 1.3523204 0.47615795
## P11554_209 1.11361441 0.35884004 1.06469143 1.1701421 1.52265480
## P11554_210 -0.51362135 -1.08909536 -0.55302107 0.3810231 -0.39598221
## P11554_211 -0.49112664 0.03867335 -0.77290097 0.6642141 -1.00829444
## P11554_212 -0.15962125 -0.56294562 0.52339236 0.5280195 -0.40876177
## P11554_213 1.50759782 0.17856303 1.15459167 0.3447799 0.90535078
## P11554_214 1.63213840 2.69080999 0.42138809 0.3718922 1.76569946
## P11554_215 0.39597610 0.82583363 1.57421692 -0.1040715 1.83300112
## P11554_216 -1.46001337 -1.20398077 -1.59885563 -1.2127096 -0.86905400
## P11554_217 -1.11057812 -0.09120888 -0.16269951 -1.1243942 0.14067567
## P11554_218 -1.58759547 -0.68813499 0.01480992 -1.1522168 -0.81039677
## P11554_225 0.29574658 -0.81967462 -1.77644692 0.9318380 -1.26379514
## P11554_226 -0.06072421 -0.49139023 -0.26071494 0.1330641 -0.82247029
## P11554_227 -0.70162298 -1.20686308 -0.90377567 0.2678905 -0.36477375
## P11554_228 -0.36971004 -0.71493122 -0.66735898 -1.2073352 -1.02865351
## P11554_229 -0.14696567 0.58602709 -0.01222251 -1.1007479 -0.42887911
## P11554_230 0.48321959 1.17063314 1.89119023 -1.6949882 -0.09533598
## AT2G47230 AT3G13510 AT5G62710 AT5G60690 AT2G44830
## P11554_207 1.1782779 1.30262488 1.5392857 0.609433897 0.80581378
## P11554_208 1.2746736 1.60711005 1.4319446 1.025417961 1.02486007
## P11554_209 1.1717015 1.22616731 1.2854779 0.726978046 1.29617783
## P11554_210 -0.6616361 -0.51955537 -0.3226055 -0.004920479 0.06069699
## P11554_211 -0.5155419 -0.37405312 -0.4641876 0.160288892 0.38397556
## P11554_212 -0.4668954 -0.25271378 -0.5979181 0.153122327 0.31616620
## P11554_213 1.5551862 1.28597982 1.2052610 1.106340436 0.93088919
## P11554_214 1.4495981 1.23821660 0.8791366 1.500158029 1.18714697
## P11554_215 1.4838396 0.90406443 1.4285698 1.261095041 0.95190328
## P11554_216 -0.4404988 -0.49121556 -0.6916353 0.097966305 -0.25297114
## P11554_217 -0.6088417 -0.27389849 -0.6113671 0.349407029 0.11301722
## P11554_218 -0.6391131 -0.07082667 -0.3887391 -0.066268727 -0.02924328
## P11554_225 -0.7398462 -0.45055733 -0.3014641 -0.856669791 -0.64414576
## P11554_226 -0.6015085 -0.61639476 -0.3008002 -0.575119201 -0.59438830
## P11554_227 -0.5664692 -0.48569855 -0.3771507 -0.497328347 -0.29637744
## P11554_228 -0.8885405 -1.52622514 -1.1322669 -1.907059087 -1.78316614
## P11554_229 -1.0595206 -0.98997895 -1.1437554 -1.320359655 -1.57373492
## P11554_230 -0.9248649 -1.51304536 -1.4377855 -1.762482677 -1.89662010
## AT2G27230 AT5G61480 AT5G43810 AT2G33860 AT3G54080
## P11554_207 0.92628602 0.71686773 1.078106753 0.64700594 0.8489459
## P11554_208 1.35114539 0.46995704 1.293367617 1.23322376 0.9817542
## P11554_209 1.43312539 1.66142938 1.637428463 1.63892601 0.7574954
## P11554_210 0.28348186 0.43833391 -0.571227883 0.11115952 -1.8740987
## P11554_211 -0.22404143 -0.05571976 -0.044726623 -1.42059070 -0.8502134
## P11554_212 -0.07059428 0.44007215 0.442939512 -0.18507643 -0.7913779
## P11554_213 1.30802503 0.79960120 0.482358113 0.55349080 1.1756606
## P11554_214 1.36107845 1.54255928 1.275407582 0.76647625 1.2606653
## P11554_215 0.24784792 0.85074852 0.265311577 1.18876297 0.5503506
## P11554_216 -0.51896222 0.71210071 -0.688008688 0.28865694 -0.2072481
## P11554_217 0.26457570 -0.05384457 -0.046085440 -0.15455706 -0.7834513
## P11554_218 -0.03906801 -0.58619764 -0.660969030 0.05143184 -0.7054176
## P11554_225 -1.25257556 -1.08093420 -0.738120266 -1.27813823 0.8755322
## P11554_226 -0.46037926 -0.73755952 0.559766566 0.46406547 0.7411367
## P11554_227 -0.33965069 -0.97987595 -0.002159109 -0.21091300 0.9279799
## P11554_228 -1.61709093 -1.21364127 -2.283075403 -1.87546219 -0.5504296
## P11554_229 -1.07136983 -1.23871281 -0.848652249 -0.26553596 -0.8678323
## P11554_230 -1.58183353 -1.68518422 -1.151661491 -1.55292592 -1.4894520
## AT1G79820 AT5G37020 AT1G12430 AT5G63950 AT1G04050
## P11554_207 0.1581543 1.4536112 1.130268852 0.24195515 -1.18808291
## P11554_208 0.7660900 0.7792609 1.042356049 1.75196736 1.52700572
## P11554_209 0.5101658 0.3462930 0.260588455 1.20202743 0.59337929
## P11554_210 -1.8000609 0.8672717 0.714572374 -0.08229845 0.06159009
## P11554_211 -0.9851449 1.6531233 0.718633594 0.41721309 0.33757959
## P11554_212 -0.4351422 0.7084768 0.937865146 0.08753884 -0.50320010
## P11554_213 1.3778828 0.1904828 0.706998070 0.42581077 1.41334991
## P11554_214 1.5969123 0.7414240 1.394024051 0.45992408 1.47239697
## P11554_215 1.3746959 0.3754656 0.610928719 1.05492810 0.74451062
## P11554_216 0.1143520 0.6061175 0.004454834 -0.12780162 0.25271306
## P11554_217 -0.4153295 -0.7515121 0.252169888 0.34619345 0.42780250
## P11554_218 -0.1791708 -0.6017411 -0.228815363 0.26118091 0.73666730
## P11554_225 0.4159793 -1.2555954 -1.313934120 -2.29152000 -1.04740623
## P11554_226 0.7456074 -1.9010650 -1.178717365 -1.81331732 -1.05056258
## P11554_227 0.3409419 -0.9515683 -1.047697886 -1.10107850 -0.87398787
## P11554_228 -1.0534296 -0.5127728 -1.120933628 -0.36245902 -1.22364533
## P11554_229 -1.3365306 -0.5087687 -1.213374567 -0.75237006 -1.59867099
## P11554_230 -1.1959730 -1.2385036 -1.669387104 0.28210578 -0.08143904
## AT2G16640 AT4G37750 AT5G67200 AT1G52310 AT1G78430 AT3G07540
## P11554_207 0.6681754 0.4504652 0.8784195 0.3347911 1.19798459 -0.04299732
## P11554_208 0.5569782 0.5426326 0.3959100 1.1593615 0.03525632 -0.05457814
## P11554_209 0.6902944 0.5738580 0.3482398 0.1920263 -0.17941563 -0.20560698
## P11554_210 0.1868968 -0.3228272 -0.2916372 -0.6373051 0.61274202 -0.06546332
## P11554_211 0.1319129 -0.3615204 -0.2556464 -0.2159094 0.06925074 -0.14112408
## P11554_212 0.1512288 -0.2609121 -0.4727112 -0.5807162 0.83672211 0.06244964
## P11554_213 1.4021818 1.5853454 1.6374005 1.0279786 0.38203448 0.93138757
## P11554_214 1.5143467 1.5893372 1.6339219 0.9177961 0.63825693 1.06159238
## P11554_215 1.0333479 1.6328643 1.6167500 1.4121368 0.65056031 0.86036085
## P11554_216 0.5251713 0.4239936 0.4518568 1.0206551 1.31271786 1.55579884
## P11554_217 0.3959585 0.4172873 0.3892172 1.2563267 1.17752343 1.52181309
## P11554_218 0.1679808 0.4468524 0.1388616 -0.1787383 0.68190954 1.24512635
## P11554_225 -0.9850780 -1.0237987 -0.8023481 -1.7476072 -0.80706366 -1.33200831
## P11554_226 -1.2216291 -1.1195121 -0.9328552 -0.2840614 -1.46256699 -1.31959155
## P11554_227 -1.4723522 -0.9051880 -0.9126182 -0.1504639 -1.31210509 -1.39645947
## P11554_228 -1.0680542 -1.2120945 -1.1655429 -1.7000081 -1.83971946 -0.86437454
## P11554_229 -1.8622212 -1.2689671 -1.3525274 -1.3909118 -1.08327738 -0.76494677
## P11554_230 -0.8151387 -1.1878159 -1.3046907 -0.4353509 -0.91081014 -1.05137822
## AT1G62360 AT5G58930 AT4G30520 AT5G03680 AT5G64340
## P11554_207 -0.28857348 -0.09739625 -1.23792720 1.10457886 -0.276784304
## P11554_208 -0.35359603 -0.40356086 0.19192144 0.17694678 -1.443748422
## P11554_209 -0.33118594 -0.40838801 0.11025213 -0.03162993 -1.237353139
## P11554_210 0.32907634 0.79781582 0.67224206 1.47718347 1.391899234
## P11554_211 0.36333371 0.57861525 1.67392327 1.14091819 1.901066276
## P11554_212 0.48448137 0.72045614 1.29726468 1.12533134 1.429554727
## P11554_213 0.08083966 -0.71569665 -0.69066438 -0.49061154 0.422574440
## P11554_214 0.35795627 -0.39813736 0.72838307 -0.01068629 -0.732651443
## P11554_215 0.25607036 0.11329756 -0.66149251 -0.71196905 0.016139400
## P11554_216 1.86336791 1.78416124 0.14370403 0.91594717 0.905710797
## P11554_217 1.62444078 1.95386522 0.45689574 0.93937172 0.243995208
## P11554_218 1.56010139 1.53063154 0.31787870 0.17893741 -0.006127085
## P11554_225 -1.66960119 -0.71242114 -0.34597774 0.32549123 0.723668531
## P11554_226 -0.83874105 -0.77394594 -0.75856714 -0.65110189 -0.478690853
## P11554_227 -0.99022961 -1.15859309 1.48977335 -0.88141211 -0.938841224
## P11554_228 -1.57618909 -1.01094230 -1.35248031 -1.81121245 0.197950857
## P11554_229 -0.18467809 -0.73734509 -0.04506474 -1.39292465 -0.742792035
## P11554_230 -0.68687331 -1.06241607 -1.99006447 -1.40315824 -1.375570965
##
## $`GO:0048519`$rowDendrogram
## 'dendrogram' with 2 branches and 46 members total, at height 2.597293
##
## $`GO:0048519`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0048519`$breaks
## [1] -2.6908100 -2.6369938 -2.5831776 -2.5293614 -2.4755452 -2.4217290
## [7] -2.3679128 -2.3140966 -2.2602804 -2.2064642 -2.1526480 -2.0988318
## [13] -2.0450156 -1.9911994 -1.9373832 -1.8835670 -1.8297508 -1.7759346
## [19] -1.7221184 -1.6683022 -1.6144860 -1.5606698 -1.5068536 -1.4530374
## [25] -1.3992212 -1.3454050 -1.2915888 -1.2377726 -1.1839564 -1.1301402
## [31] -1.0763240 -1.0225078 -0.9686916 -0.9148754 -0.8610592 -0.8072430
## [37] -0.7534268 -0.6996106 -0.6457944 -0.5919782 -0.5381620 -0.4843458
## [43] -0.4305296 -0.3767134 -0.3228972 -0.2690810 -0.2152648 -0.1614486
## [49] -0.1076324 -0.0538162 0.0000000 0.0538162 0.1076324 0.1614486
## [55] 0.2152648 0.2690810 0.3228972 0.3767134 0.4305296 0.4843458
## [61] 0.5381620 0.5919782 0.6457944 0.6996106 0.7534268 0.8072430
## [67] 0.8610592 0.9148754 0.9686916 1.0225078 1.0763240 1.1301402
## [73] 1.1839564 1.2377726 1.2915888 1.3454050 1.3992212 1.4530374
## [79] 1.5068536 1.5606698 1.6144860 1.6683022 1.7221184 1.7759346
## [85] 1.8297508 1.8835670 1.9373832 1.9911994 2.0450156 2.0988318
## [91] 2.1526480 2.2064642 2.2602804 2.3140966 2.3679128 2.4217290
## [97] 2.4755452 2.5293614 2.5831776 2.6369938 2.6908100
##
## $`GO:0048519`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0048519`$colorTable
## low high color
## 1 -2.6908100 -2.6369938 #0000FF
## 2 -2.6369938 -2.5831776 #0505FF
## 3 -2.5831776 -2.5293614 #0A0AFF
## 4 -2.5293614 -2.4755452 #0F0FFF
## 5 -2.4755452 -2.4217290 #1414FF
## 6 -2.4217290 -2.3679128 #1919FF
## 7 -2.3679128 -2.3140966 #1E1EFF
## 8 -2.3140966 -2.2602804 #2424FF
## 9 -2.2602804 -2.2064642 #2929FF
## 10 -2.2064642 -2.1526480 #2E2EFF
## 11 -2.1526480 -2.0988318 #3333FF
## 12 -2.0988318 -2.0450156 #3838FF
## 13 -2.0450156 -1.9911994 #3D3DFF
## 14 -1.9911994 -1.9373832 #4242FF
## 15 -1.9373832 -1.8835670 #4848FF
## 16 -1.8835670 -1.8297508 #4D4DFF
## 17 -1.8297508 -1.7759346 #5252FF
## 18 -1.7759346 -1.7221184 #5757FF
## 19 -1.7221184 -1.6683022 #5C5CFF
## 20 -1.6683022 -1.6144860 #6161FF
## 21 -1.6144860 -1.5606698 #6767FF
## 22 -1.5606698 -1.5068536 #6C6CFF
## 23 -1.5068536 -1.4530374 #7171FF
## 24 -1.4530374 -1.3992212 #7676FF
## 25 -1.3992212 -1.3454050 #7B7BFF
## 26 -1.3454050 -1.2915888 #8080FF
## 27 -1.2915888 -1.2377726 #8585FF
## 28 -1.2377726 -1.1839564 #8B8BFF
## 29 -1.1839564 -1.1301402 #9090FF
## 30 -1.1301402 -1.0763240 #9595FF
## 31 -1.0763240 -1.0225078 #9A9AFF
## 32 -1.0225078 -0.9686916 #9F9FFF
## 33 -0.9686916 -0.9148754 #A4A4FF
## 34 -0.9148754 -0.8610592 #AAAAFF
## 35 -0.8610592 -0.8072430 #AFAFFF
## 36 -0.8072430 -0.7534268 #B4B4FF
## 37 -0.7534268 -0.6996106 #B9B9FF
## 38 -0.6996106 -0.6457944 #BEBEFF
## 39 -0.6457944 -0.5919782 #C3C3FF
## 40 -0.5919782 -0.5381620 #C8C8FF
## 41 -0.5381620 -0.4843458 #CECEFF
## 42 -0.4843458 -0.4305296 #D3D3FF
## 43 -0.4305296 -0.3767134 #D8D8FF
## 44 -0.3767134 -0.3228972 #DDDDFF
## 45 -0.3228972 -0.2690810 #E2E2FF
## 46 -0.2690810 -0.2152648 #E7E7FF
## 47 -0.2152648 -0.1614486 #ECECFF
## 48 -0.1614486 -0.1076324 #F2F2FF
## 49 -0.1076324 -0.0538162 #F7F7FF
## 50 -0.0538162 0.0000000 #FCFCFF
## 51 0.0000000 0.0538162 #FFFCFC
## 52 0.0538162 0.1076324 #FFF7F7
## 53 0.1076324 0.1614486 #FFF2F2
## 54 0.1614486 0.2152648 #FFECEC
## 55 0.2152648 0.2690810 #FFE7E7
## 56 0.2690810 0.3228972 #FFE2E2
## 57 0.3228972 0.3767134 #FFDDDD
## 58 0.3767134 0.4305296 #FFD8D8
## 59 0.4305296 0.4843458 #FFD3D3
## 60 0.4843458 0.5381620 #FFCECE
## 61 0.5381620 0.5919782 #FFC8C8
## 62 0.5919782 0.6457944 #FFC3C3
## 63 0.6457944 0.6996106 #FFBEBE
## 64 0.6996106 0.7534268 #FFB9B9
## 65 0.7534268 0.8072430 #FFB4B4
## 66 0.8072430 0.8610592 #FFAFAF
## 67 0.8610592 0.9148754 #FFA9A9
## 68 0.9148754 0.9686916 #FFA4A4
## 69 0.9686916 1.0225078 #FF9F9F
## 70 1.0225078 1.0763240 #FF9A9A
## 71 1.0763240 1.1301402 #FF9595
## 72 1.1301402 1.1839564 #FF9090
## 73 1.1839564 1.2377726 #FF8B8B
## 74 1.2377726 1.2915888 #FF8585
## 75 1.2915888 1.3454050 #FF8080
## 76 1.3454050 1.3992212 #FF7B7B
## 77 1.3992212 1.4530374 #FF7676
## 78 1.4530374 1.5068536 #FF7171
## 79 1.5068536 1.5606698 #FF6C6C
## 80 1.5606698 1.6144860 #FF6767
## 81 1.6144860 1.6683022 #FF6161
## 82 1.6683022 1.7221184 #FF5C5C
## 83 1.7221184 1.7759346 #FF5757
## 84 1.7759346 1.8297508 #FF5252
## 85 1.8297508 1.8835670 #FF4D4D
## 86 1.8835670 1.9373832 #FF4848
## 87 1.9373832 1.9911994 #FF4242
## 88 1.9911994 2.0450156 #FF3D3D
## 89 2.0450156 2.0988318 #FF3838
## 90 2.0988318 2.1526480 #FF3333
## 91 2.1526480 2.2064642 #FF2E2E
## 92 2.2064642 2.2602804 #FF2929
## 93 2.2602804 2.3140966 #FF2424
## 94 2.3140966 2.3679128 #FF1E1E
## 95 2.3679128 2.4217290 #FF1919
## 96 2.4217290 2.4755452 #FF1414
## 97 2.4755452 2.5293614 #FF0F0F
## 98 2.5293614 2.5831776 #FF0A0A
## 99 2.5831776 2.6369938 #FF0505
## 100 2.6369938 2.6908100 #FF0000
##
## $`GO:0048519`$layout
## $`GO:0048519`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0048519`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0048519`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0016458`
## $`GO:0016458`$rowInd
## [1] 27 48 46 19 57 38 47 32 7 54 29 3 8 52 49 6 2 9 40 39 30 18 12 25 10
## [26] 35 41 15 36 11 21 53 17 4 23 26 16 56 22 14 28 51 33 58 42 20 45 13 50 34
## [51] 37 55 44 43 5 1 31 24
##
## $`GO:0016458`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0016458`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0016458`$carpet
## AT3G02470 AT5G15510 AT5G14620 AT2G22610 AT5G63110
## P11554_207 -1.05119951 -0.008810111 -1.4402367 -1.36745670 -1.1813311
## P11554_208 -0.87172398 0.137158802 -1.1381411 -0.87677558 -1.1124271
## P11554_209 -0.29645663 0.358734496 -1.7750591 -0.95925543 -0.4600816
## P11554_210 1.30431898 1.628832850 0.6241171 1.02236520 0.8593594
## P11554_211 1.47336629 0.616464286 0.5823754 0.65782655 0.1622171
## P11554_212 1.70406847 2.282115087 1.1252871 0.87951265 0.6936841
## P11554_213 0.22533705 -1.652713659 -1.0014063 -1.89890622 -0.2689967
## P11554_214 0.03590086 -0.750123637 -0.6184812 -0.98418924 -2.0700372
## P11554_215 -0.46155720 -1.707972606 -1.0889238 -1.29070094 -1.7986601
## P11554_216 -0.13366946 -1.117242626 -0.2393719 0.88051902 0.8790115
## P11554_217 0.06326516 0.251549599 0.2906166 1.34237928 0.9552237
## P11554_218 0.14713438 -0.180107582 1.2218766 0.83517277 1.1195221
## P11554_225 -1.18312449 0.099012948 1.8081848 -0.24961633 -0.3811741
## P11554_226 -1.45423299 -0.687654629 0.2052824 0.29259658 0.6799717
## P11554_227 -1.46592682 -0.093377073 0.7190811 0.01107019 0.4225871
## P11554_228 0.76722824 -0.029175231 0.2504544 0.44533115 1.2489370
## P11554_229 1.30353940 0.110688578 -0.1334735 0.11327936 0.1395636
## P11554_230 -0.10626777 0.742620508 0.6078181 1.14684768 0.1126307
## AT4G11130 AT5G15380 AT3G23890 AT1G44110 AT5G55520
## P11554_207 -1.20817116 0.203458684 0.4747263 0.93283443 1.1708965
## P11554_208 -0.29313899 0.436918257 1.2923942 1.35918495 0.5590836
## P11554_209 -0.80268859 0.699101380 0.9777198 1.05602781 0.9127344
## P11554_210 0.26695250 0.015095822 0.4539379 0.62617353 0.5372966
## P11554_211 0.59170956 -0.958582919 0.1975577 0.42756483 0.1777599
## P11554_212 1.09483597 0.310937072 0.4311020 0.32853271 0.5738915
## P11554_213 -1.60393167 0.007447376 0.6447525 0.47831372 0.4235760
## P11554_214 -1.22732848 0.698405854 1.1789711 1.07093151 1.2030406
## P11554_215 -1.92313413 -0.129202752 0.6397487 0.46625017 0.4634155
## P11554_216 0.07155204 0.350749612 0.6002678 0.70911173 0.6705350
## P11554_217 -0.01775822 0.674685835 0.6567489 0.15044727 0.4995766
## P11554_218 -0.22752745 0.549861653 0.3635734 0.09817155 0.7051998
## P11554_225 0.46684278 -2.314936075 -1.4533920 -1.02018349 -1.0957572
## P11554_226 0.71905725 0.812217995 -1.4584113 -1.56596547 -1.2795542
## P11554_227 0.54404742 1.446889949 -1.0705713 -0.97802545 -1.5928805
## P11554_228 1.34182452 0.135355873 -1.2887196 -1.55503602 -1.3120804
## P11554_229 1.31423443 -2.314936075 -1.4728318 -1.01909161 -0.9373455
## P11554_230 0.89262221 -0.623467542 -1.1675742 -1.56524216 -1.6793882
## AT3G14190 AT1G05440 AT1G50240 AT5G49020 AT5G37010
## P11554_207 1.19637262 0.6913499 -0.08751811 0.1083347 0.72078871
## P11554_208 1.31651840 1.0107677 0.64935806 0.1937203 1.04372553
## P11554_209 0.91568087 1.4406834 0.68484050 0.4239454 -0.18762944
## P11554_210 0.78317796 0.9525019 0.11043846 0.2607693 0.99665889
## P11554_211 0.73935087 0.5252172 0.40245607 0.6001044 0.46034421
## P11554_212 0.80548209 -0.1010815 0.37674859 0.6130614 1.05882153
## P11554_213 0.72966616 1.3052538 0.76813298 0.2755085 0.27104474
## P11554_214 0.50166650 0.2793860 0.85666416 1.2198504 0.64354392
## P11554_215 -0.39429283 0.2978220 0.77533929 1.1080049 0.06643999
## P11554_216 0.40058689 0.2821980 1.08648986 1.0982299 0.93683936
## P11554_217 0.08980679 0.5395334 0.96786955 0.7538363 0.67130308
## P11554_218 0.25444068 0.2336478 0.94345103 0.8301483 0.91376449
## P11554_225 -1.46293034 -0.9852936 -1.96266255 -2.1559805 -1.37497204
## P11554_226 -1.58069430 -1.4383497 -1.63877405 -1.4052181 -1.52708912
## P11554_227 -1.06738510 -1.0729914 -1.04281336 -0.8471498 -1.10098078
## P11554_228 -1.49152379 -0.9503456 -1.29195009 -1.4025120 -1.07326932
## P11554_229 -0.36500120 -1.8992611 -0.42350696 -0.8695165 -0.70554546
## P11554_230 -1.37092228 -1.1110385 -1.17456343 -0.8051370 -1.81378831
## AT1G34355 AT1G03780 AT1G53140 AT4G22860 AT4G20910
## P11554_207 0.24804861 0.53760813 0.39175714 0.769142076 0.2286444
## P11554_208 0.41249520 0.75933169 0.78179429 0.691982764 0.9364704
## P11554_209 -0.01991303 0.81923249 0.43484096 0.125140231 0.7384526
## P11554_210 0.64174815 0.03242994 0.22532923 -0.004603819 -1.1259642
## P11554_211 0.48999551 0.39711162 -0.00813146 0.341413634 -0.6422914
## P11554_212 0.92099743 0.75816240 0.95345150 0.888930613 -0.5604655
## P11554_213 0.95520235 0.85744856 1.11920677 1.070392409 1.2835512
## P11554_214 0.45922760 0.66439273 1.06008994 0.871442902 0.7781553
## P11554_215 0.69784078 0.98226037 0.45497863 1.263928526 0.9060881
## P11554_216 1.36247064 0.93583105 1.00133897 0.615895371 -1.6546271
## P11554_217 0.91982736 0.71227313 1.01435747 0.840128593 -1.4122696
## P11554_218 0.69497838 0.56033352 0.21395967 0.166336455 -1.4278292
## P11554_225 -1.05633582 -1.25754505 -1.36682438 -1.409570459 0.8962905
## P11554_226 -1.72969005 -1.39697666 -1.14082651 -1.133563311 0.9466315
## P11554_227 -1.32848374 -1.01536198 -0.99607502 -1.274756717 0.9394540
## P11554_228 -1.35965654 -1.40545682 -1.59591057 -1.791297051 0.4817486
## P11554_229 -0.94739114 -1.35447664 -0.78051764 -0.681037560 -0.7306285
## P11554_230 -1.36136171 -1.58659848 -1.76281900 -1.349904656 -0.5814111
## AT3G20260 AT2G07170 AT1G63640 AT2G36200 AT1G59540
## P11554_207 1.356989112 1.16246877 0.65362148 0.789928494 0.89838602
## P11554_208 0.450287346 1.21521868 1.19793097 1.147157823 0.90761152
## P11554_209 0.298735970 1.21044060 0.66940459 1.240633443 0.85293264
## P11554_210 -0.056798598 -0.66107760 0.03018073 -0.023104453 -0.21382820
## P11554_211 -0.228332034 -0.12282299 0.11017199 -0.068006674 -0.18095297
## P11554_212 0.164737388 0.10803380 0.41654947 -0.008155888 0.13412257
## P11554_213 1.092446644 0.86065807 1.36595007 1.286910857 1.09666630
## P11554_214 1.339114000 1.47539009 1.35216418 1.451908875 1.77799150
## P11554_215 1.933467847 1.28567065 1.42003958 1.477508447 0.92163613
## P11554_216 0.304804141 -0.12647254 -0.05780029 -0.450342300 0.63155658
## P11554_217 0.008421198 0.05602871 -0.33709362 -0.267145883 0.33528696
## P11554_218 -0.164368265 0.23599004 0.21448053 -0.051833089 -0.06332676
## P11554_225 -0.622980957 -1.08364674 -1.16443712 -1.305396182 -1.31176673
## P11554_226 -1.373246245 -1.05232203 -1.22178465 -1.301268083 -0.83269463
## P11554_227 -1.113826203 -1.13010657 -1.55998944 -1.127871684 -1.43072396
## P11554_228 -1.034404668 -1.31162882 -1.35670972 -1.059346613 -1.52820159
## P11554_229 -0.638317165 -1.24453093 -0.81421892 -0.846733569 -0.87351120
## P11554_230 -1.716729512 -0.87729120 -0.91845984 -0.884843523 -1.12118416
## AT3G44050 AT4G26760 AT1G72250 AT3G51290 AT1G63470
## P11554_207 0.49062690 0.49237815 0.42812565 0.7964021 0.39827854
## P11554_208 1.44409164 1.02412101 1.44250027 0.5880725 0.72631587
## P11554_209 0.91545785 0.99777421 1.55304695 0.5335597 0.78423093
## P11554_210 -0.18305242 -0.22102436 -0.09069569 -0.1891357 -0.89809460
## P11554_211 -0.06699018 0.51842659 -0.38790248 0.2865837 -0.86570646
## P11554_212 0.31037187 -0.02816597 0.74583226 -0.1605962 -0.23404125
## P11554_213 1.41877855 1.11003081 0.40512159 1.3796540 1.12779060
## P11554_214 1.38927405 1.73901972 0.75619977 2.4027910 1.45144030
## P11554_215 0.92845116 1.21610106 0.76009427 0.7243514 2.39794751
## P11554_216 -0.23321926 -0.67844688 0.35010657 -0.2606224 -0.05419263
## P11554_217 0.14388483 -0.16629505 0.32174792 -0.3599353 -0.08785984
## P11554_218 0.04572015 -0.07629223 0.65321710 -0.6509858 -0.13224827
## P11554_225 -0.59927425 -0.61236862 -0.49392693 -1.1450880 -0.60672659
## P11554_226 -1.19753963 -1.10117486 -0.92000145 -0.7236093 0.15292517
## P11554_227 -0.65550479 -0.75218325 -0.82299784 -0.4278338 -0.92178326
## P11554_228 -1.91806737 -2.31365568 -2.03087407 -0.5410209 -1.38938201
## P11554_229 -1.57705282 -0.58290669 -1.64056304 -0.1462212 -0.76576286
## P11554_230 -0.65595628 -0.56533796 -1.02903083 -2.1063658 -1.08313112
## AT2G27040 AT5G49160 AT2G01120 AT1G08130 AT2G31650 AT2G42120
## P11554_207 0.41763475 1.16458835 1.3673048 1.0704173 0.9828711 0.9923037
## P11554_208 0.80432846 1.33503206 1.1245187 1.1235339 1.2924367 1.4416298
## P11554_209 0.97810208 1.33869939 1.3054209 1.4451343 1.4791522 1.4332230
## P11554_210 -0.80293132 -0.89386386 -0.6195260 -0.6183257 -0.9227062 -0.1428372
## P11554_211 -0.64779678 -0.83606417 -0.7211546 -0.4854937 -0.3913605 -0.3603117
## P11554_212 -0.42616786 -0.81260899 -0.1387222 -0.4523754 -0.6331581 -0.4765925
## P11554_213 1.79610316 1.31897871 1.3720305 1.3467417 1.4200196 1.0734640
## P11554_214 1.49547662 1.40369442 1.4692400 1.4970461 1.2678466 0.9746974
## P11554_215 1.67298644 1.36143996 1.4273952 1.5858800 1.6092564 1.7990594
## P11554_216 -0.33735093 -0.97870971 -0.8347709 -0.8514475 -0.9042858 -0.8005728
## P11554_217 0.24673487 -0.98081851 -0.8541389 -0.8167845 -0.7721309 -0.1910451
## P11554_218 -0.07633598 -0.89684827 -0.5658507 -0.7682538 -0.7183550 -0.8727801
## P11554_225 -0.57290586 -0.15778068 -0.9684401 -0.7710146 -0.6499586 -0.7574585
## P11554_226 -0.37937398 -0.09579880 -0.4686177 -0.3396039 -0.3604688 -0.3602489
## P11554_227 -0.36750535 -0.09725883 -0.5927264 -0.4455129 -0.3056104 -0.3393199
## P11554_228 -1.17399648 -0.78394688 -1.0442281 -0.6249507 -0.7020533 -1.2666587
## P11554_229 -1.09200549 -0.71419694 -0.7369275 -1.0783912 -1.0152369 -1.0887502
## P11554_230 -1.53499634 -0.67453726 -0.5208069 -0.8165994 -0.6762583 -1.0578018
## AT1G78770 AT5G62410 AT2G31270 AT1G69770 AT3G06930 AT5G48600
## P11554_207 1.0911893 0.9984663 1.3302474 1.2168231 1.0361988 1.1850839
## P11554_208 1.3025314 1.1344067 1.1977920 1.1287121 1.0531032 1.4112412
## P11554_209 1.3054000 1.2260337 1.0730228 1.1008244 1.1196234 1.2979243
## P11554_210 -0.3948275 -0.5818279 -0.3970551 -0.4566175 -0.4899215 -0.4601231
## P11554_211 -0.4746138 -0.4330440 -0.4924679 -0.5338723 -0.5805870 -0.5431664
## P11554_212 -0.4556716 -0.3687862 -0.3826736 -0.5311471 -0.4381157 -0.3626244
## P11554_213 1.1728965 1.1374980 1.4371205 1.5417596 1.5013435 1.3788438
## P11554_214 1.4445825 1.6968836 1.4683452 1.5372370 1.5409616 1.3865620
## P11554_215 1.6174674 1.6769697 1.5002337 1.5402341 1.5979495 1.4561109
## P11554_216 -0.7129891 -0.7732624 -0.4672640 -0.4820198 -0.3310363 -0.6694035
## P11554_217 -0.4645472 -0.1240111 -0.6042890 -0.5217882 -0.4974818 -0.5402411
## P11554_218 -0.4224507 -0.3218926 -0.5407428 -0.5244628 -0.3211456 -0.5947747
## P11554_225 -1.3014420 -0.7931206 -0.5467487 -0.6429901 -0.5331245 -0.8902324
## P11554_226 -0.4293049 -0.6897992 -0.6233182 -0.6681518 -0.5116349 -0.6540643
## P11554_227 -0.4588290 -0.6167416 -0.6736884 -0.6942066 -0.5610192 -0.5556733
## P11554_228 -1.1003175 -1.0435267 -1.0264521 -0.9726310 -1.1989506 -1.0114518
## P11554_229 -1.0351118 -1.1572843 -1.2234305 -1.0494889 -1.2535412 -0.9858013
## P11554_230 -0.6839622 -0.9669614 -1.0286311 -0.9882142 -1.1326217 -0.8482098
## AT3G24495 AT5G63960 AT4G30860 AT2G24490 AT5G08020 AT1G67630
## P11554_207 1.1759085 1.1713245 1.2598948 1.3906610 1.3098072 1.2757878
## P11554_208 1.3129506 1.4549063 1.2403666 1.2687255 1.2122490 1.4147095
## P11554_209 1.3620853 1.2718754 1.3010537 1.2807546 1.2485153 1.4695292
## P11554_210 -0.5086609 -0.4380328 -0.6242655 -0.5998294 -0.6317226 -0.5756564
## P11554_211 -0.5744437 -0.3767061 -0.6209217 -0.5995103 -0.5633658 -0.5893138
## P11554_212 -0.3793020 -0.1143842 -0.5137401 -0.5244005 -0.5783329 -0.5027818
## P11554_213 1.4568398 1.3679954 1.4751910 1.3542183 1.3925527 1.3049248
## P11554_214 1.3683543 1.3458729 1.3536179 1.3539319 1.4851550 1.3345465
## P11554_215 1.4233484 1.3777394 1.4328099 1.4659468 1.4855806 1.3331947
## P11554_216 -0.4544018 -0.7198209 -0.7992458 -0.6457795 -0.5645983 -0.6739194
## P11554_217 -0.6087522 -0.6517789 -0.6683867 -0.4058549 -0.6002815 -0.6655967
## P11554_218 -0.5533049 -0.5775556 -0.3873341 -0.4858176 -0.5847791 -0.6449196
## P11554_225 -0.7099810 -0.8001198 -0.6189537 -0.6618007 -0.4472875 -0.5866447
## P11554_226 -0.6408921 -0.7574147 -0.4748843 -0.5631934 -0.5694748 -0.4694051
## P11554_227 -0.6273739 -0.4070590 -0.2779060 -0.6241822 -0.6568106 -0.4650593
## P11554_228 -0.9496034 -1.1241694 -1.0382718 -0.9212376 -0.9987128 -0.9482895
## P11554_229 -1.0748779 -1.0238247 -0.9835280 -0.9274583 -0.9780567 -1.0463365
## P11554_230 -1.0178932 -0.9988476 -1.0554962 -1.1551737 -0.9604372 -0.9647698
## AT5G46280 AT3G42660 AT3G56870 AT5G58130 AT4G39630 AT4G33400
## P11554_207 1.2840035 1.2026529 1.0857548 1.4331919 1.02647377 1.0377675
## P11554_208 1.4012114 1.3543728 1.2818245 0.9594619 1.30862283 1.3307120
## P11554_209 1.3744306 1.3296797 1.0363244 0.7339383 0.83845930 0.6999784
## P11554_210 -0.6071882 -0.5845479 -0.5998170 -0.6547731 -0.79199267 -0.6473562
## P11554_211 -0.5419400 -0.5147894 -0.5952130 -0.7782167 -0.74361044 -0.5105969
## P11554_212 -0.5738425 -0.4083394 -0.4732082 -0.7555671 -0.46455499 -0.3410567
## P11554_213 1.2893939 1.3344438 1.6817398 1.6484543 1.57109110 1.7688255
## P11554_214 1.3415019 1.3634470 1.5408901 1.6000720 1.48010081 1.6508338
## P11554_215 1.4349610 1.4178038 1.4512960 1.6259530 1.55162575 1.3147365
## P11554_216 -0.4993116 -0.6261368 -0.8063276 -0.7142931 -0.20646988 -0.3756472
## P11554_217 -0.5836650 -0.4915054 -0.4851773 -0.5365953 -0.11366298 -0.1402530
## P11554_218 -0.6696976 -0.5518063 -0.7737659 -0.5813396 -0.07837407 -0.3951485
## P11554_225 -0.5530158 -0.4524528 -0.4604306 -0.3192966 -0.74846427 -1.1358228
## P11554_226 -0.5130034 -0.4968942 -0.6266917 -0.6935828 -0.70785048 -0.8962147
## P11554_227 -0.5526989 -0.4386445 -0.6421350 -0.8417391 -0.73462818 -0.7408285
## P11554_228 -0.9780033 -1.0858299 -0.6901882 -0.6302850 -0.94580201 -0.9997533
## P11554_229 -1.0929475 -1.1435044 -1.0785735 -0.6550591 -1.11229676 -0.7306821
## P11554_230 -0.9601884 -1.2079490 -0.8463015 -0.8403239 -1.12866685 -0.8894938
## AT1G09450 AT1G01370 AT3G22780 AT2G32590
## P11554_207 1.14067060 1.0774924 0.5648621 0.9158040
## P11554_208 1.01761081 0.9760469 0.5787601 1.1134653
## P11554_209 0.45465578 1.3844050 1.3331534 1.2933929
## P11554_210 -0.89141769 -0.2086459 -0.2123467 -0.7870728
## P11554_211 -0.09576789 -0.5515003 -0.5302097 -0.1643060
## P11554_212 -0.22788708 -0.5661568 -0.3613878 -0.2244563
## P11554_213 1.65709160 1.6468283 1.3574660 1.4311164
## P11554_214 1.79001639 1.1982197 1.5148655 1.1000030
## P11554_215 1.55472045 1.6721586 2.0534306 1.7474341
## P11554_216 -0.31097454 -0.5492081 -0.2543973 -0.3377033
## P11554_217 -0.65062580 -0.4413494 -0.2292852 -0.5916351
## P11554_218 -0.34015336 -0.5609742 -0.2746607 -0.1548873
## P11554_225 -0.63725106 -0.8324846 -0.8399609 -1.3558185
## P11554_226 -1.21314308 -0.9305390 -0.8689236 -0.9238693
## P11554_227 -0.76254832 -0.5722250 -0.5007497 -0.6470324
## P11554_228 -0.91513172 -1.1861148 -1.4326832 -1.4871688
## P11554_229 -0.59930136 -0.6316731 -0.9439907 -0.4577732
## P11554_230 -0.97056373 -0.9242798 -0.9539423 -0.4694927
##
## $`GO:0016458`$rowDendrogram
## 'dendrogram' with 2 branches and 58 members total, at height 2.475988
##
## $`GO:0016458`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0016458`$breaks
## [1] -2.40279104 -2.35473522 -2.30667940 -2.25862357 -2.21056775 -2.16251193
## [7] -2.11445611 -2.06640029 -2.01834447 -1.97028865 -1.92223283 -1.87417701
## [13] -1.82612119 -1.77806537 -1.73000955 -1.68195373 -1.63389790 -1.58584208
## [19] -1.53778626 -1.48973044 -1.44167462 -1.39361880 -1.34556298 -1.29750716
## [25] -1.24945134 -1.20139552 -1.15333970 -1.10528388 -1.05722806 -1.00917224
## [31] -0.96111641 -0.91306059 -0.86500477 -0.81694895 -0.76889313 -0.72083731
## [37] -0.67278149 -0.62472567 -0.57666985 -0.52861403 -0.48055821 -0.43250239
## [43] -0.38444657 -0.33639075 -0.28833492 -0.24027910 -0.19222328 -0.14416746
## [49] -0.09611164 -0.04805582 0.00000000 0.04805582 0.09611164 0.14416746
## [55] 0.19222328 0.24027910 0.28833492 0.33639075 0.38444657 0.43250239
## [61] 0.48055821 0.52861403 0.57666985 0.62472567 0.67278149 0.72083731
## [67] 0.76889313 0.81694895 0.86500477 0.91306059 0.96111641 1.00917224
## [73] 1.05722806 1.10528388 1.15333970 1.20139552 1.24945134 1.29750716
## [79] 1.34556298 1.39361880 1.44167462 1.48973044 1.53778626 1.58584208
## [85] 1.63389790 1.68195373 1.73000955 1.77806537 1.82612119 1.87417701
## [91] 1.92223283 1.97028865 2.01834447 2.06640029 2.11445611 2.16251193
## [97] 2.21056775 2.25862357 2.30667940 2.35473522 2.40279104
##
## $`GO:0016458`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0016458`$colorTable
## low high color
## 1 -2.40279104 -2.35473522 #0000FF
## 2 -2.35473522 -2.30667940 #0505FF
## 3 -2.30667940 -2.25862357 #0A0AFF
## 4 -2.25862357 -2.21056775 #0F0FFF
## 5 -2.21056775 -2.16251193 #1414FF
## 6 -2.16251193 -2.11445611 #1919FF
## 7 -2.11445611 -2.06640029 #1E1EFF
## 8 -2.06640029 -2.01834447 #2424FF
## 9 -2.01834447 -1.97028865 #2929FF
## 10 -1.97028865 -1.92223283 #2E2EFF
## 11 -1.92223283 -1.87417701 #3333FF
## 12 -1.87417701 -1.82612119 #3838FF
## 13 -1.82612119 -1.77806537 #3D3DFF
## 14 -1.77806537 -1.73000955 #4242FF
## 15 -1.73000955 -1.68195373 #4848FF
## 16 -1.68195373 -1.63389790 #4D4DFF
## 17 -1.63389790 -1.58584208 #5252FF
## 18 -1.58584208 -1.53778626 #5757FF
## 19 -1.53778626 -1.48973044 #5C5CFF
## 20 -1.48973044 -1.44167462 #6161FF
## 21 -1.44167462 -1.39361880 #6767FF
## 22 -1.39361880 -1.34556298 #6C6CFF
## 23 -1.34556298 -1.29750716 #7171FF
## 24 -1.29750716 -1.24945134 #7676FF
## 25 -1.24945134 -1.20139552 #7B7BFF
## 26 -1.20139552 -1.15333970 #8080FF
## 27 -1.15333970 -1.10528388 #8585FF
## 28 -1.10528388 -1.05722806 #8B8BFF
## 29 -1.05722806 -1.00917224 #9090FF
## 30 -1.00917224 -0.96111641 #9595FF
## 31 -0.96111641 -0.91306059 #9A9AFF
## 32 -0.91306059 -0.86500477 #9F9FFF
## 33 -0.86500477 -0.81694895 #A4A4FF
## 34 -0.81694895 -0.76889313 #AAAAFF
## 35 -0.76889313 -0.72083731 #AFAFFF
## 36 -0.72083731 -0.67278149 #B4B4FF
## 37 -0.67278149 -0.62472567 #B9B9FF
## 38 -0.62472567 -0.57666985 #BEBEFF
## 39 -0.57666985 -0.52861403 #C3C3FF
## 40 -0.52861403 -0.48055821 #C8C8FF
## 41 -0.48055821 -0.43250239 #CECEFF
## 42 -0.43250239 -0.38444657 #D3D3FF
## 43 -0.38444657 -0.33639075 #D8D8FF
## 44 -0.33639075 -0.28833492 #DDDDFF
## 45 -0.28833492 -0.24027910 #E2E2FF
## 46 -0.24027910 -0.19222328 #E7E7FF
## 47 -0.19222328 -0.14416746 #ECECFF
## 48 -0.14416746 -0.09611164 #F2F2FF
## 49 -0.09611164 -0.04805582 #F7F7FF
## 50 -0.04805582 0.00000000 #FCFCFF
## 51 0.00000000 0.04805582 #FFFCFC
## 52 0.04805582 0.09611164 #FFF7F7
## 53 0.09611164 0.14416746 #FFF2F2
## 54 0.14416746 0.19222328 #FFECEC
## 55 0.19222328 0.24027910 #FFE7E7
## 56 0.24027910 0.28833492 #FFE2E2
## 57 0.28833492 0.33639075 #FFDDDD
## 58 0.33639075 0.38444657 #FFD8D8
## 59 0.38444657 0.43250239 #FFD3D3
## 60 0.43250239 0.48055821 #FFCECE
## 61 0.48055821 0.52861403 #FFC8C8
## 62 0.52861403 0.57666985 #FFC3C3
## 63 0.57666985 0.62472567 #FFBEBE
## 64 0.62472567 0.67278149 #FFB9B9
## 65 0.67278149 0.72083731 #FFB4B4
## 66 0.72083731 0.76889313 #FFAFAF
## 67 0.76889313 0.81694895 #FFA9A9
## 68 0.81694895 0.86500477 #FFA4A4
## 69 0.86500477 0.91306059 #FF9F9F
## 70 0.91306059 0.96111641 #FF9A9A
## 71 0.96111641 1.00917224 #FF9595
## 72 1.00917224 1.05722806 #FF9090
## 73 1.05722806 1.10528388 #FF8B8B
## 74 1.10528388 1.15333970 #FF8585
## 75 1.15333970 1.20139552 #FF8080
## 76 1.20139552 1.24945134 #FF7B7B
## 77 1.24945134 1.29750716 #FF7676
## 78 1.29750716 1.34556298 #FF7171
## 79 1.34556298 1.39361880 #FF6C6C
## 80 1.39361880 1.44167462 #FF6767
## 81 1.44167462 1.48973044 #FF6161
## 82 1.48973044 1.53778626 #FF5C5C
## 83 1.53778626 1.58584208 #FF5757
## 84 1.58584208 1.63389790 #FF5252
## 85 1.63389790 1.68195373 #FF4D4D
## 86 1.68195373 1.73000955 #FF4848
## 87 1.73000955 1.77806537 #FF4242
## 88 1.77806537 1.82612119 #FF3D3D
## 89 1.82612119 1.87417701 #FF3838
## 90 1.87417701 1.92223283 #FF3333
## 91 1.92223283 1.97028865 #FF2E2E
## 92 1.97028865 2.01834447 #FF2929
## 93 2.01834447 2.06640029 #FF2424
## 94 2.06640029 2.11445611 #FF1E1E
## 95 2.11445611 2.16251193 #FF1919
## 96 2.16251193 2.21056775 #FF1414
## 97 2.21056775 2.25862357 #FF0F0F
## 98 2.25862357 2.30667940 #FF0A0A
## 99 2.30667940 2.35473522 #FF0505
## 100 2.35473522 2.40279104 #FF0000
##
## $`GO:0016458`$layout
## $`GO:0016458`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0016458`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0016458`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0010608`
## $`GO:0010608`$rowInd
## [1] 1 2
##
## $`GO:0010608`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0010608`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0010608`$carpet
## AT4G08980 AT4G21320
## P11554_207 -0.75660003 -0.45300927
## P11554_208 -0.68255147 -0.17878025
## P11554_209 -1.02410016 -0.59781456
## P11554_210 0.94244160 -0.51658085
## P11554_211 0.75798528 -0.84925185
## P11554_212 0.02061941 -0.92612083
## P11554_213 -1.42390879 -0.16905352
## P11554_214 -1.61572126 -0.33599388
## P11554_215 -1.63855666 -1.00565228
## P11554_216 0.28437632 -0.34833703
## P11554_217 0.13118648 -1.13647494
## P11554_218 0.01221541 -0.43813691
## P11554_225 0.97611498 1.67838792
## P11554_226 0.53815502 2.56647892
## P11554_227 0.21688168 1.04267927
## P11554_228 1.97309219 0.88941729
## P11554_229 0.73384262 0.05965655
## P11554_230 0.55452739 0.71858623
##
## $`GO:0010608`$rowDendrogram
## 'dendrogram' with 2 branches and 2 members total, at height 0.2780001
##
## $`GO:0010608`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0010608`$breaks
## [1] -2.56647892 -2.51514934 -2.46381977 -2.41249019 -2.36116061 -2.30983103
## [7] -2.25850145 -2.20717187 -2.15584229 -2.10451272 -2.05318314 -2.00185356
## [13] -1.95052398 -1.89919440 -1.84786482 -1.79653525 -1.74520567 -1.69387609
## [19] -1.64254651 -1.59121693 -1.53988735 -1.48855777 -1.43722820 -1.38589862
## [25] -1.33456904 -1.28323946 -1.23190988 -1.18058030 -1.12925073 -1.07792115
## [31] -1.02659157 -0.97526199 -0.92393241 -0.87260283 -0.82127326 -0.76994368
## [37] -0.71861410 -0.66728452 -0.61595494 -0.56462536 -0.51329578 -0.46196621
## [43] -0.41063663 -0.35930705 -0.30797747 -0.25664789 -0.20531831 -0.15398874
## [49] -0.10265916 -0.05132958 0.00000000 0.05132958 0.10265916 0.15398874
## [55] 0.20531831 0.25664789 0.30797747 0.35930705 0.41063663 0.46196621
## [61] 0.51329578 0.56462536 0.61595494 0.66728452 0.71861410 0.76994368
## [67] 0.82127326 0.87260283 0.92393241 0.97526199 1.02659157 1.07792115
## [73] 1.12925073 1.18058030 1.23190988 1.28323946 1.33456904 1.38589862
## [79] 1.43722820 1.48855777 1.53988735 1.59121693 1.64254651 1.69387609
## [85] 1.74520567 1.79653525 1.84786482 1.89919440 1.95052398 2.00185356
## [91] 2.05318314 2.10451272 2.15584229 2.20717187 2.25850145 2.30983103
## [97] 2.36116061 2.41249019 2.46381977 2.51514934 2.56647892
##
## $`GO:0010608`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0010608`$colorTable
## low high color
## 1 -2.56647892 -2.51514934 #0000FF
## 2 -2.51514934 -2.46381977 #0505FF
## 3 -2.46381977 -2.41249019 #0A0AFF
## 4 -2.41249019 -2.36116061 #0F0FFF
## 5 -2.36116061 -2.30983103 #1414FF
## 6 -2.30983103 -2.25850145 #1919FF
## 7 -2.25850145 -2.20717187 #1E1EFF
## 8 -2.20717187 -2.15584229 #2424FF
## 9 -2.15584229 -2.10451272 #2929FF
## 10 -2.10451272 -2.05318314 #2E2EFF
## 11 -2.05318314 -2.00185356 #3333FF
## 12 -2.00185356 -1.95052398 #3838FF
## 13 -1.95052398 -1.89919440 #3D3DFF
## 14 -1.89919440 -1.84786482 #4242FF
## 15 -1.84786482 -1.79653525 #4848FF
## 16 -1.79653525 -1.74520567 #4D4DFF
## 17 -1.74520567 -1.69387609 #5252FF
## 18 -1.69387609 -1.64254651 #5757FF
## 19 -1.64254651 -1.59121693 #5C5CFF
## 20 -1.59121693 -1.53988735 #6161FF
## 21 -1.53988735 -1.48855777 #6767FF
## 22 -1.48855777 -1.43722820 #6C6CFF
## 23 -1.43722820 -1.38589862 #7171FF
## 24 -1.38589862 -1.33456904 #7676FF
## 25 -1.33456904 -1.28323946 #7B7BFF
## 26 -1.28323946 -1.23190988 #8080FF
## 27 -1.23190988 -1.18058030 #8585FF
## 28 -1.18058030 -1.12925073 #8B8BFF
## 29 -1.12925073 -1.07792115 #9090FF
## 30 -1.07792115 -1.02659157 #9595FF
## 31 -1.02659157 -0.97526199 #9A9AFF
## 32 -0.97526199 -0.92393241 #9F9FFF
## 33 -0.92393241 -0.87260283 #A4A4FF
## 34 -0.87260283 -0.82127326 #AAAAFF
## 35 -0.82127326 -0.76994368 #AFAFFF
## 36 -0.76994368 -0.71861410 #B4B4FF
## 37 -0.71861410 -0.66728452 #B9B9FF
## 38 -0.66728452 -0.61595494 #BEBEFF
## 39 -0.61595494 -0.56462536 #C3C3FF
## 40 -0.56462536 -0.51329578 #C8C8FF
## 41 -0.51329578 -0.46196621 #CECEFF
## 42 -0.46196621 -0.41063663 #D3D3FF
## 43 -0.41063663 -0.35930705 #D8D8FF
## 44 -0.35930705 -0.30797747 #DDDDFF
## 45 -0.30797747 -0.25664789 #E2E2FF
## 46 -0.25664789 -0.20531831 #E7E7FF
## 47 -0.20531831 -0.15398874 #ECECFF
## 48 -0.15398874 -0.10265916 #F2F2FF
## 49 -0.10265916 -0.05132958 #F7F7FF
## 50 -0.05132958 0.00000000 #FCFCFF
## 51 0.00000000 0.05132958 #FFFCFC
## 52 0.05132958 0.10265916 #FFF7F7
## 53 0.10265916 0.15398874 #FFF2F2
## 54 0.15398874 0.20531831 #FFECEC
## 55 0.20531831 0.25664789 #FFE7E7
## 56 0.25664789 0.30797747 #FFE2E2
## 57 0.30797747 0.35930705 #FFDDDD
## 58 0.35930705 0.41063663 #FFD8D8
## 59 0.41063663 0.46196621 #FFD3D3
## 60 0.46196621 0.51329578 #FFCECE
## 61 0.51329578 0.56462536 #FFC8C8
## 62 0.56462536 0.61595494 #FFC3C3
## 63 0.61595494 0.66728452 #FFBEBE
## 64 0.66728452 0.71861410 #FFB9B9
## 65 0.71861410 0.76994368 #FFB4B4
## 66 0.76994368 0.82127326 #FFAFAF
## 67 0.82127326 0.87260283 #FFA9A9
## 68 0.87260283 0.92393241 #FFA4A4
## 69 0.92393241 0.97526199 #FF9F9F
## 70 0.97526199 1.02659157 #FF9A9A
## 71 1.02659157 1.07792115 #FF9595
## 72 1.07792115 1.12925073 #FF9090
## 73 1.12925073 1.18058030 #FF8B8B
## 74 1.18058030 1.23190988 #FF8585
## 75 1.23190988 1.28323946 #FF8080
## 76 1.28323946 1.33456904 #FF7B7B
## 77 1.33456904 1.38589862 #FF7676
## 78 1.38589862 1.43722820 #FF7171
## 79 1.43722820 1.48855777 #FF6C6C
## 80 1.48855777 1.53988735 #FF6767
## 81 1.53988735 1.59121693 #FF6161
## 82 1.59121693 1.64254651 #FF5C5C
## 83 1.64254651 1.69387609 #FF5757
## 84 1.69387609 1.74520567 #FF5252
## 85 1.74520567 1.79653525 #FF4D4D
## 86 1.79653525 1.84786482 #FF4848
## 87 1.84786482 1.89919440 #FF4242
## 88 1.89919440 1.95052398 #FF3D3D
## 89 1.95052398 2.00185356 #FF3838
## 90 2.00185356 2.05318314 #FF3333
## 91 2.05318314 2.10451272 #FF2E2E
## 92 2.10451272 2.15584229 #FF2929
## 93 2.15584229 2.20717187 #FF2424
## 94 2.20717187 2.25850145 #FF1E1E
## 95 2.25850145 2.30983103 #FF1919
## 96 2.30983103 2.36116061 #FF1414
## 97 2.36116061 2.41249019 #FF0F0F
## 98 2.41249019 2.46381977 #FF0A0A
## 99 2.46381977 2.51514934 #FF0505
## 100 2.51514934 2.56647892 #FF0000
##
## $`GO:0010608`$layout
## $`GO:0010608`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0010608`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0010608`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0007059`
## $`GO:0007059`$rowInd
## [1] 11 33 32 6 20 2 26 17 21 9 40 39 36 3 23 14 19 22 15 5 12 1 24 27 13
## [26] 25 42 35 4 30 8 18 31 37 41 16 29 38 7 28 10 34
##
## $`GO:0007059`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0007059`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0007059`$carpet
## AT2G32900 AT5G12260 AT5G08450 AT1G70510 AT3G47950
## P11554_207 -1.19693166 -1.54004627 -1.47962192 -1.01131630 -1.169284615
## P11554_208 -1.75391100 -1.28788054 -0.89919221 -1.56447815 -0.692490694
## P11554_209 -0.66119402 -1.54623420 -1.04902843 -1.33033933 -0.278356343
## P11554_210 -0.39900824 0.11900228 -0.39162610 0.88088994 -0.222741195
## P11554_211 0.49172827 -0.44283925 0.07653797 0.46887833 0.205568854
## P11554_212 0.10613364 -0.09774761 0.75662635 1.62836124 -0.009028352
## P11554_213 -0.33035726 -1.11539059 -0.73175110 -1.01291010 -0.382855823
## P11554_214 -0.80127861 0.44547319 -0.32950300 -0.74597588 -2.423957257
## P11554_215 0.40001860 0.18290228 -0.34526474 -1.53663203 -1.256759313
## P11554_216 0.19268910 -0.43714300 0.87604753 0.19304709 0.515203128
## P11554_217 -1.01882587 0.70088444 1.19934628 0.32637763 0.013799432
## P11554_218 -0.52090315 -0.39219730 0.71174786 1.36583023 0.365041023
## P11554_225 1.46649391 1.87788020 -0.98492518 -0.46303259 0.048194653
## P11554_226 1.97454087 1.16128174 0.51807011 0.58362602 0.222725026
## P11554_227 1.75295303 1.16250474 -0.61932480 0.03432441 1.550669160
## P11554_228 0.07774632 0.84151787 -0.74475484 0.64035419 1.286945200
## P11554_229 0.45027569 -0.53865544 1.16494518 0.80902353 0.672019922
## P11554_230 -0.23016962 0.90668747 2.27167104 0.73397176 1.555307195
## AT1G63990 AT4G16440 AT3G13170 AT3G48190 AT2G03430 AT5G61460
## P11554_207 -1.0819733 0.9109396 0.8452952 -1.77477657 -0.64387454 0.1690030
## P11554_208 1.5028218 1.0012075 0.9286599 -0.21023818 0.76057955 0.5745332
## P11554_209 -0.2122820 0.1954302 0.5583977 1.00886386 1.08338791 0.4296886
## P11554_210 0.7888017 -2.2096651 -1.0124865 -0.90368515 -0.58271925 -1.1566688
## P11554_211 1.0662396 -1.1421248 -1.1203453 -1.31731613 -0.44720304 -1.3100682
## P11554_212 0.5564114 -0.9835008 -0.5345785 0.16135563 -1.01665127 -0.9219234
## P11554_213 -0.8173164 -0.3500896 -0.1577089 -0.73511169 -0.19880019 0.1434596
## P11554_214 -0.8484475 0.2892436 0.7883983 -0.15680781 0.04166522 0.3320849
## P11554_215 -0.1849842 1.6423301 1.1567461 -0.16563591 -0.64706158 0.2835217
## P11554_216 0.2448448 -0.4663315 -1.2434783 -1.18961856 -1.70223351 -1.6677165
## P11554_217 0.9731614 -0.2039709 -1.7331162 -0.46042218 -1.20536341 -1.4624459
## P11554_218 0.4966269 -0.4977975 -1.1619559 -0.06536888 -1.26267499 -1.2568870
## P11554_225 -2.5365512 -0.9868317 1.2562533 0.40073269 0.35384292 0.9054863
## P11554_226 -0.5970184 0.3090278 0.4033785 0.76311391 1.77737545 1.0073601
## P11554_227 1.2066453 -0.3289292 1.2755456 2.12908261 1.06493726 1.0946348
## P11554_228 -0.2449562 0.2420137 -0.8290287 0.60035603 0.77131047 0.8349256
## P11554_229 0.3056214 1.2504948 0.7575585 0.45008873 0.67743293 0.7664692
## P11554_230 -0.6176448 1.3285538 -0.1775347 1.46538761 1.17605008 1.2345427
## AT5G60110 AT5G18950 AT1G67420 AT3G54670 AT3G02680
## P11554_207 2.50928529 1.01617268 0.05198693 0.29214044 -0.28017788
## P11554_208 1.39850023 0.01265348 0.66191644 0.42064404 2.39270590
## P11554_209 1.26569457 -0.90486223 1.22152543 0.44202327 -0.56568425
## P11554_210 -0.02577165 0.35286424 1.05473582 0.37481972 0.12152621
## P11554_211 -0.49670016 -0.23416569 -0.08753393 -0.45033855 0.15866195
## P11554_212 0.19673336 -1.15241560 0.25336875 -0.36294041 1.55634665
## P11554_213 -1.22003841 1.46229257 -0.82549498 0.09372032 0.38247647
## P11554_214 -0.71371252 1.52937480 1.54521641 1.70436760 1.36025311
## P11554_215 -0.64027016 -0.22429098 0.61970382 1.55650292 0.42988827
## P11554_216 0.56102680 0.03520998 0.01482800 -0.47295597 -1.35906994
## P11554_217 0.44251010 -0.22224424 -0.59102142 0.14964522 -0.33903137
## P11554_218 -1.27838650 0.17753089 -2.37132935 -0.87611812 -0.39877862
## P11554_225 0.03830225 1.22026475 -1.12276113 -2.40973424 -0.57233015
## P11554_226 -0.02373941 -0.86618536 -0.34146161 -0.36814618 0.05430749
## P11554_227 -1.11101377 -1.56972940 1.34066794 -1.10940449 -1.14029395
## P11554_228 0.35994006 1.46067770 0.09812408 0.59936324 -0.82864952
## P11554_229 -0.89973492 -1.08970044 -0.99961527 -0.81605642 -1.29906503
## P11554_230 -0.36262517 -1.00344715 -0.52285592 1.23246762 0.32691468
## AT3G23890 AT3G48210 AT3G10270 AT1G69630 AT2G42720
## P11554_207 0.4747263 1.30189975 0.55884982 0.94097871 1.15274500
## P11554_208 1.2923942 1.30438718 1.08468650 0.45053961 1.12352388
## P11554_209 0.9777198 1.12887609 1.62749954 0.92260053 0.67990822
## P11554_210 0.4539379 0.33979780 -1.22894318 1.50916671 -0.04238059
## P11554_211 0.1975577 0.37155971 -0.18492336 0.20228865 -1.55926718
## P11554_212 0.4311020 0.42079045 -0.12129483 -1.04006536 -1.18067164
## P11554_213 0.6447525 -0.07135348 0.71105235 0.94075607 0.94179016
## P11554_214 1.1789711 0.29037019 0.02182673 -0.26578949 1.78311563
## P11554_215 0.6397487 1.34515165 1.77685262 1.98300407 1.64433051
## P11554_216 0.6002678 -0.05617984 0.34116044 -1.65419735 -0.41073085
## P11554_217 0.6567489 0.41949725 0.53380971 -0.17589654 -0.20972536
## P11554_218 0.3635734 -0.01418174 0.37842203 0.05545678 -1.23054980
## P11554_225 -1.4533920 -2.16352833 -0.76788776 -0.59589431 -0.31727510
## P11554_226 -1.4584113 -0.77206931 -0.67569562 -0.75586967 -0.04918682
## P11554_227 -1.0705713 -1.54726235 -1.19163950 -0.35369930 -0.80778999
## P11554_228 -1.2887196 -0.66009859 -1.97064664 0.22270384 -0.26614453
## P11554_229 -1.4728318 -0.38705532 -0.03012431 -1.02878503 -0.70479387
## P11554_230 -1.1675742 -1.25060113 -0.86300453 -1.35729792 -0.54689768
## AT1G50270 AT3G58210 AT4G17380 AT3G01410 AT3G61340
## P11554_207 1.8486276 -0.12253114 0.32580518 0.89537650 1.25149071
## P11554_208 1.0244050 1.03978493 1.33493705 0.73350723 0.86560227
## P11554_209 0.1162557 0.64868924 0.98355817 0.54101711 1.13222556
## P11554_210 0.6201343 -0.74994763 0.16701465 -0.27804284 -0.64029527
## P11554_211 -0.5713815 -1.00638078 -0.85867033 -0.44141105 -0.21916169
## P11554_212 -0.3236314 -0.22091364 0.29328110 -0.87512306 -0.80859676
## P11554_213 0.1984109 1.89863228 1.44880725 1.66530601 1.66661888
## P11554_214 1.9306451 1.89200147 1.34965526 1.73806214 1.31538863
## P11554_215 0.9750136 0.87743695 1.35471814 1.76062799 1.14837100
## P11554_216 -0.6299528 -1.02416284 -1.01282974 -0.52267308 0.01147291
## P11554_217 -0.9216412 0.42886318 -0.36400533 -0.65867593 0.11036858
## P11554_218 -1.3743764 -0.94783538 0.02623413 0.01597894 0.02712737
## P11554_225 0.4094586 -0.35393820 -0.14992908 -1.05782733 -0.41843931
## P11554_226 -0.4697676 -0.58406053 -0.12586442 -0.19526072 -0.68099504
## P11554_227 -1.7151617 -1.23056062 -0.52926344 -0.39038789 -1.12253970
## P11554_228 -0.2787312 -1.16433597 -1.58662763 -1.52572007 -0.91447041
## P11554_229 -0.6337507 0.65985576 -1.40941472 -0.47396013 -1.41364846
## P11554_230 -0.2045564 -0.04059709 -1.24740623 -0.93079382 -1.31051927
## AT5G65180 AT5G18810 AT1G67690 AT5G04130 AT1G79890 AT3G20475
## P11554_207 1.0901691 1.4908843 0.8371584 1.0702445 1.2056138 1.3679832
## P11554_208 1.2351624 1.1061465 1.3813777 1.2493431 1.0268523 1.0780559
## P11554_209 0.7689245 0.9977039 1.3499552 1.1168326 1.4416254 1.1629068
## P11554_210 -0.4538456 -0.5545175 -0.4357500 -0.5271782 -0.3988507 -0.8046798
## P11554_211 -0.6647288 -0.4608549 -1.1143086 -0.2318507 -0.7065301 -0.6463421
## P11554_212 -0.3454711 -0.4025878 -0.4501572 -0.1325102 -0.3357253 -0.3828723
## P11554_213 2.0025262 1.8829576 1.1970683 1.4242057 1.4038974 1.8402779
## P11554_214 1.6856641 0.8025901 1.7362130 1.4414487 1.6161444 1.1953351
## P11554_215 0.9974153 1.4770543 1.3790813 1.4368750 1.2699177 1.2563516
## P11554_216 -1.1469946 -0.3588351 -0.3820097 -0.1169846 -0.4224643 -0.5931881
## P11554_217 -0.4237974 -0.5001784 -0.3641219 -0.4244547 -0.7139891 -0.5122333
## P11554_218 -0.4825678 -0.4546359 -0.6262387 -0.2268235 -0.6843908 -0.2708118
## P11554_225 -0.7092009 -0.7806279 -0.9596258 -1.1856024 -0.2710567 -0.6308978
## P11554_226 -0.6292903 -0.8340000 -0.2564725 -0.9242380 -0.7154143 -0.2945882
## P11554_227 -0.4820260 -1.0238544 -0.4420835 -0.7918354 -0.6199425 -0.5600096
## P11554_228 -0.5513323 -0.7057090 -1.0753125 -1.1974295 -1.2978335 -1.2766234
## P11554_229 -1.2007440 -1.4127435 -0.8638316 -0.9983122 -0.7977086 -1.0921583
## P11554_230 -0.6898628 -0.2687922 -0.9109419 -0.9817301 -1.0001450 -0.8365060
## AT5G07660 AT5G48600 AT5G63920 AT3G10690 AT5G04110 AT5G57880
## P11554_207 1.2489549 1.1850839 1.1110978 1.1172395 1.1324380 1.542746472
## P11554_208 1.5530785 1.4112412 1.3349649 1.2201710 1.2236215 0.339784338
## P11554_209 1.0678267 1.2979243 1.4055262 1.2485323 1.1084209 1.439313449
## P11554_210 -0.5562306 -0.4601231 -0.5359858 -0.5977639 -0.4675613 0.267472917
## P11554_211 -0.5788684 -0.5431664 -0.5269688 -0.6266575 -0.4030146 -0.125525992
## P11554_212 -0.3248160 -0.3626244 -0.3857805 -0.4796994 -0.5424438 -0.006885189
## P11554_213 1.5205099 1.3788438 1.3414047 1.4091492 1.6178900 1.061308161
## P11554_214 1.1882190 1.3865620 1.5132862 1.4355288 1.4823474 1.438043312
## P11554_215 1.5131207 1.4561109 1.3596463 1.6310324 1.4997431 1.007007997
## P11554_216 -0.7627030 -0.6694035 -0.5300699 -0.4004922 -0.5299081 -0.501863766
## P11554_217 -0.8524258 -0.5402411 -0.5065896 -0.4627756 -0.6370566 -1.353167199
## P11554_218 -0.6409672 -0.5947747 -0.4046068 -0.4285505 -0.5397953 -0.519782469
## P11554_225 -0.8694127 -0.8902324 -0.7656418 -0.7269294 -0.6318833 -1.937149859
## P11554_226 -0.4358695 -0.6540643 -0.6934622 -0.5981473 -0.6965451 -0.031514074
## P11554_227 -0.7069094 -0.5556733 -0.6733024 -0.7213687 -0.6486021 -1.066138767
## P11554_228 -1.0280267 -1.0114518 -1.1549999 -1.0530173 -0.9509846 -0.715476766
## P11554_229 -0.7422745 -0.9858013 -1.0363476 -0.9104149 -1.1334433 -0.295329754
## P11554_230 -0.5932058 -0.8482098 -0.8521707 -1.0558367 -0.8832228 -0.542842812
## AT1G72270 AT4G35520 AT2G27170 AT5G15920
## P11554_207 1.5074254 1.03731889 1.1614486 0.980447541
## P11554_208 1.3130577 1.51895097 1.4230079 1.493339090
## P11554_209 1.3511359 1.92672732 1.2904145 0.690155686
## P11554_210 -0.4096606 -0.29266537 -0.5521039 -0.412868695
## P11554_211 -0.4095291 0.08706676 -0.1502148 -0.316369855
## P11554_212 -0.1375077 -0.03653568 -0.1566788 0.002796631
## P11554_213 0.4855110 1.38158346 0.8561628 1.186285126
## P11554_214 1.8159623 0.97771678 1.3861563 1.580953974
## P11554_215 0.9837054 0.80479466 1.5715921 1.399090575
## P11554_216 0.1021732 -0.95233375 -0.5870010 -0.393701180
## P11554_217 -0.5097416 -0.82224508 -0.4865800 -0.168197399
## P11554_218 -0.5183853 -0.66738276 -0.3690833 -0.049899161
## P11554_225 -0.9609499 -1.09431314 -1.4835051 -1.602892032
## P11554_226 -0.8155169 -0.98583571 -1.2378370 -1.010320364
## P11554_227 -0.6354613 -0.70383867 -0.9138657 -1.061562706
## P11554_228 -1.0967536 -0.67371441 -0.5955745 -0.471088286
## P11554_229 -0.5556710 -0.84607737 -0.8745139 -1.352528930
## P11554_230 -1.5097940 -0.65921689 -0.2818241 -0.493640016
##
## $`GO:0007059`$rowDendrogram
## 'dendrogram' with 2 branches and 42 members total, at height 2.232392
##
## $`GO:0007059`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0007059`$breaks
## [1] -2.53655125 -2.48582022 -2.43508920 -2.38435817 -2.33362715 -2.28289612
## [7] -2.23216510 -2.18143407 -2.13070305 -2.07997202 -2.02924100 -1.97850997
## [13] -1.92777895 -1.87704792 -1.82631690 -1.77558587 -1.72485485 -1.67412382
## [19] -1.62339280 -1.57266177 -1.52193075 -1.47119972 -1.42046870 -1.36973767
## [25] -1.31900665 -1.26827562 -1.21754460 -1.16681357 -1.11608255 -1.06535152
## [31] -1.01462050 -0.96388947 -0.91315845 -0.86242742 -0.81169640 -0.76096537
## [37] -0.71023435 -0.65950332 -0.60877230 -0.55804127 -0.50731025 -0.45657922
## [43] -0.40584820 -0.35511717 -0.30438615 -0.25365512 -0.20292410 -0.15219307
## [49] -0.10146205 -0.05073102 0.00000000 0.05073102 0.10146205 0.15219307
## [55] 0.20292410 0.25365512 0.30438615 0.35511717 0.40584820 0.45657922
## [61] 0.50731025 0.55804127 0.60877230 0.65950332 0.71023435 0.76096537
## [67] 0.81169640 0.86242742 0.91315845 0.96388947 1.01462050 1.06535152
## [73] 1.11608255 1.16681357 1.21754460 1.26827562 1.31900665 1.36973767
## [79] 1.42046870 1.47119972 1.52193075 1.57266177 1.62339280 1.67412382
## [85] 1.72485485 1.77558587 1.82631690 1.87704792 1.92777895 1.97850997
## [91] 2.02924100 2.07997202 2.13070305 2.18143407 2.23216510 2.28289612
## [97] 2.33362715 2.38435817 2.43508920 2.48582022 2.53655125
##
## $`GO:0007059`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0007059`$colorTable
## low high color
## 1 -2.53655125 -2.48582022 #0000FF
## 2 -2.48582022 -2.43508920 #0505FF
## 3 -2.43508920 -2.38435817 #0A0AFF
## 4 -2.38435817 -2.33362715 #0F0FFF
## 5 -2.33362715 -2.28289612 #1414FF
## 6 -2.28289612 -2.23216510 #1919FF
## 7 -2.23216510 -2.18143407 #1E1EFF
## 8 -2.18143407 -2.13070305 #2424FF
## 9 -2.13070305 -2.07997202 #2929FF
## 10 -2.07997202 -2.02924100 #2E2EFF
## 11 -2.02924100 -1.97850997 #3333FF
## 12 -1.97850997 -1.92777895 #3838FF
## 13 -1.92777895 -1.87704792 #3D3DFF
## 14 -1.87704792 -1.82631690 #4242FF
## 15 -1.82631690 -1.77558587 #4848FF
## 16 -1.77558587 -1.72485485 #4D4DFF
## 17 -1.72485485 -1.67412382 #5252FF
## 18 -1.67412382 -1.62339280 #5757FF
## 19 -1.62339280 -1.57266177 #5C5CFF
## 20 -1.57266177 -1.52193075 #6161FF
## 21 -1.52193075 -1.47119972 #6767FF
## 22 -1.47119972 -1.42046870 #6C6CFF
## 23 -1.42046870 -1.36973767 #7171FF
## 24 -1.36973767 -1.31900665 #7676FF
## 25 -1.31900665 -1.26827562 #7B7BFF
## 26 -1.26827562 -1.21754460 #8080FF
## 27 -1.21754460 -1.16681357 #8585FF
## 28 -1.16681357 -1.11608255 #8B8BFF
## 29 -1.11608255 -1.06535152 #9090FF
## 30 -1.06535152 -1.01462050 #9595FF
## 31 -1.01462050 -0.96388947 #9A9AFF
## 32 -0.96388947 -0.91315845 #9F9FFF
## 33 -0.91315845 -0.86242742 #A4A4FF
## 34 -0.86242742 -0.81169640 #AAAAFF
## 35 -0.81169640 -0.76096537 #AFAFFF
## 36 -0.76096537 -0.71023435 #B4B4FF
## 37 -0.71023435 -0.65950332 #B9B9FF
## 38 -0.65950332 -0.60877230 #BEBEFF
## 39 -0.60877230 -0.55804127 #C3C3FF
## 40 -0.55804127 -0.50731025 #C8C8FF
## 41 -0.50731025 -0.45657922 #CECEFF
## 42 -0.45657922 -0.40584820 #D3D3FF
## 43 -0.40584820 -0.35511717 #D8D8FF
## 44 -0.35511717 -0.30438615 #DDDDFF
## 45 -0.30438615 -0.25365512 #E2E2FF
## 46 -0.25365512 -0.20292410 #E7E7FF
## 47 -0.20292410 -0.15219307 #ECECFF
## 48 -0.15219307 -0.10146205 #F2F2FF
## 49 -0.10146205 -0.05073102 #F7F7FF
## 50 -0.05073102 0.00000000 #FCFCFF
## 51 0.00000000 0.05073102 #FFFCFC
## 52 0.05073102 0.10146205 #FFF7F7
## 53 0.10146205 0.15219307 #FFF2F2
## 54 0.15219307 0.20292410 #FFECEC
## 55 0.20292410 0.25365512 #FFE7E7
## 56 0.25365512 0.30438615 #FFE2E2
## 57 0.30438615 0.35511717 #FFDDDD
## 58 0.35511717 0.40584820 #FFD8D8
## 59 0.40584820 0.45657922 #FFD3D3
## 60 0.45657922 0.50731025 #FFCECE
## 61 0.50731025 0.55804127 #FFC8C8
## 62 0.55804127 0.60877230 #FFC3C3
## 63 0.60877230 0.65950332 #FFBEBE
## 64 0.65950332 0.71023435 #FFB9B9
## 65 0.71023435 0.76096537 #FFB4B4
## 66 0.76096537 0.81169640 #FFAFAF
## 67 0.81169640 0.86242742 #FFA9A9
## 68 0.86242742 0.91315845 #FFA4A4
## 69 0.91315845 0.96388947 #FF9F9F
## 70 0.96388947 1.01462050 #FF9A9A
## 71 1.01462050 1.06535152 #FF9595
## 72 1.06535152 1.11608255 #FF9090
## 73 1.11608255 1.16681357 #FF8B8B
## 74 1.16681357 1.21754460 #FF8585
## 75 1.21754460 1.26827562 #FF8080
## 76 1.26827562 1.31900665 #FF7B7B
## 77 1.31900665 1.36973767 #FF7676
## 78 1.36973767 1.42046870 #FF7171
## 79 1.42046870 1.47119972 #FF6C6C
## 80 1.47119972 1.52193075 #FF6767
## 81 1.52193075 1.57266177 #FF6161
## 82 1.57266177 1.62339280 #FF5C5C
## 83 1.62339280 1.67412382 #FF5757
## 84 1.67412382 1.72485485 #FF5252
## 85 1.72485485 1.77558587 #FF4D4D
## 86 1.77558587 1.82631690 #FF4848
## 87 1.82631690 1.87704792 #FF4242
## 88 1.87704792 1.92777895 #FF3D3D
## 89 1.92777895 1.97850997 #FF3838
## 90 1.97850997 2.02924100 #FF3333
## 91 2.02924100 2.07997202 #FF2E2E
## 92 2.07997202 2.13070305 #FF2929
## 93 2.13070305 2.18143407 #FF2424
## 94 2.18143407 2.23216510 #FF1E1E
## 95 2.23216510 2.28289612 #FF1919
## 96 2.28289612 2.33362715 #FF1414
## 97 2.33362715 2.38435817 #FF0F0F
## 98 2.38435817 2.43508920 #FF0A0A
## 99 2.43508920 2.48582022 #FF0505
## 100 2.48582022 2.53655125 #FF0000
##
## $`GO:0007059`$layout
## $`GO:0007059`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0007059`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0007059`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0051301`
## $`GO:0051301`$rowInd
## [1] 3 10 57 26 6 56 50 64 45 16 54 69 18 41 27 21 22 55 71 17 29 47 53 65 74
## [26] 60 70 12 23 34 5 1 48 43 63 68 67 52 39 44 59 51 42 46 24 13 38 2 11 58
## [51] 15 9 61 36 62 32 35 8 20 14 28 25 31 37 19 40 72 73 66 7 30 33 4 49
##
## $`GO:0051301`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0051301`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0051301`$carpet
## AT1G13980 AT1G56350 AT4G30080 AT2G44190 AT1G48410
## P11554_207 -2.02583091 0.05597583 -0.02004782 0.02359938 -1.52185850
## P11554_208 -0.20041671 -0.43149410 -0.26278260 0.09597322 0.05451137
## P11554_209 -0.77853339 0.89216461 -0.14882417 -0.11751802 0.29427536
## P11554_210 1.37517789 0.14658224 0.83865422 0.66339577 -1.20210992
## P11554_211 0.60232073 1.46649752 0.60461351 1.35345693 -1.01390535
## P11554_212 1.00262403 0.40344901 0.68022917 0.52050707 -0.17301048
## P11554_213 -0.11012221 2.18600030 0.17257126 -0.04625256 0.48140777
## P11554_214 0.27832275 0.36738448 0.75705191 -0.28248273 0.93994463
## P11554_215 -0.65343346 0.35603822 -0.02358148 -0.13526557 0.46290840
## P11554_216 0.73486940 1.15975672 1.62721135 1.62573798 0.73776929
## P11554_217 0.83286493 -0.67708219 1.39469401 1.46636470 1.72800670
## P11554_218 -0.07013975 -0.15642626 1.12173902 0.57292648 1.12843318
## P11554_225 1.89485945 -0.47482011 -1.44695738 -0.76362532 -1.93815311
## P11554_226 -1.12244910 -1.15597632 -1.62982454 -2.05398874 -0.82091856
## P11554_227 0.09660717 -0.89260776 -1.63662941 -1.85712639 0.47505566
## P11554_228 0.07147299 -1.79814904 -0.40203256 0.20954856 -0.70839668
## P11554_229 -0.45833267 -1.01726171 -0.74319097 -0.86552132 0.20531390
## P11554_230 -1.46986114 -0.43003145 -0.88289354 -0.40972946 0.87072635
## AT4G26740 AT4G03240 AT5G15540 AT4G00150 AT1G78580 AT4G21800
## P11554_207 -0.5052412 -0.7780148 0.50622693 0.54985365 -0.1750517 0.75300430
## P11554_208 -0.5052412 0.4453293 1.60179206 0.24737007 1.1377001 1.22746442
## P11554_209 -0.5052412 0.1171017 0.89996375 0.01148859 0.9926790 1.39238146
## P11554_210 -0.5052412 -0.9914645 0.02002549 0.23778851 1.4102571 0.96792346
## P11554_211 -0.5052412 -0.1958370 -0.47800680 -0.06570887 1.3100664 -0.21283066
## P11554_212 -0.5052412 0.9297783 1.07368450 2.57765367 1.3142760 0.46157872
## P11554_213 -0.5052412 0.2478037 -0.09223314 1.22091714 -0.5517982 0.30849479
## P11554_214 2.4562049 1.1554786 0.04969077 -0.83822176 0.9309133 0.57418187
## P11554_215 -0.5052412 0.8084441 0.66905538 -1.08914640 -0.3919688 1.29496809
## P11554_216 1.9647210 0.2602740 -1.85836392 0.50900187 -0.4560700 -0.91028829
## P11554_217 -0.5052412 -2.7365670 -2.10724346 -1.08727008 -0.3980925 -0.99511114
## P11554_218 -0.5052412 -1.1356889 -1.43258638 -0.97489268 0.7549452 -0.47512285
## P11554_225 -0.5052412 0.4073613 0.63580391 -0.34691682 -0.8474471 -1.84499542
## P11554_226 -0.5052412 -0.5052130 -0.10201199 0.54432011 -0.8051162 -1.00990221
## P11554_227 1.2384123 -0.3514988 -0.50690603 -1.32882176 -1.8048390 -1.73897148
## P11554_228 -0.5052412 0.2119025 0.24771539 0.48799436 -1.1307170 -0.22619247
## P11554_229 -0.5052412 0.5155110 -0.04656693 -1.20083311 -0.2829498 0.37939276
## P11554_230 1.4140379 1.5952997 0.91996045 0.54542352 -1.0067866 0.05402464
## AT5G27540 AT2G20000 AT3G59420 AT2G44950 AT2G34710
## P11554_207 -0.003296869 -0.25898756 0.42694502 0.4900622 1.26674556
## P11554_208 -0.002503470 -0.23855749 0.18773868 1.1115269 0.90672661
## P11554_209 1.689562293 0.61776725 0.86407768 1.0886149 1.43933069
## P11554_210 -0.985319881 -0.37899176 0.26081816 -0.4606751 -0.08884232
## P11554_211 -1.468707789 -1.31015858 -0.10258101 0.3570595 -0.61131914
## P11554_212 -0.149352211 -0.88722495 0.09698469 1.2492092 -0.02289997
## P11554_213 1.865794290 1.48362485 1.75151915 0.9285465 1.01836971
## P11554_214 0.976521702 0.97046793 -0.46488134 0.3151900 1.73925127
## P11554_215 1.495195162 1.61365014 0.93136951 1.6156572 0.85363252
## P11554_216 -1.208254913 -1.61797650 -1.79415625 -1.0052641 0.30859762
## P11554_217 -1.092607158 -0.07872542 0.07070032 -0.7933688 -0.70656298
## P11554_218 -0.064722875 -0.46877238 0.73245553 -1.3730689 -0.82758621
## P11554_225 -0.375129925 0.43620663 -0.11666044 -0.4757028 -0.46916182
## P11554_226 0.361240460 1.09939566 -0.41463830 -0.5190658 -0.88198622
## P11554_227 0.440412765 0.97868799 -1.79415625 -0.2919003 -0.63047876
## P11554_228 -0.955794081 -0.90810742 -0.02949492 -1.5057745 -1.54602210
## P11554_229 -0.536600828 -1.39831549 -1.79415625 -1.4205892 -0.26719085
## P11554_230 0.013563327 0.34601710 1.18811601 0.6895433 -1.48060359
## AT2G34780 AT4G22970 AT5G40770 AT1G80620 AT2G47420 AT4G01560
## P11554_207 0.9040177 1.0147745 0.9927272 1.0182398 1.0669535 1.0476259
## P11554_208 1.1254688 1.0247614 1.2503838 1.3144156 1.2993738 1.1122329
## P11554_209 1.1427176 1.0334445 1.1668868 1.1141369 1.0293368 1.2261864
## P11554_210 -0.3438493 -0.4749653 -0.4859794 -0.7624893 -0.6780071 -0.6973430
## P11554_211 -0.3378913 -0.6539722 -0.5692513 -0.4683782 -0.3963653 -0.6785019
## P11554_212 -0.3331456 -0.0966451 -0.4953855 -0.5599108 -0.7769252 -0.4968660
## P11554_213 1.5416957 1.5440869 1.4794205 1.3903009 1.4552934 1.5076958
## P11554_214 1.3400337 1.5993432 1.3871415 1.4361724 1.6483672 1.4035466
## P11554_215 1.6765209 1.6275016 1.5440418 1.6058363 1.3765885 1.7132453
## P11554_216 -0.4370116 -0.7503155 -0.2935312 -0.3827245 -0.3763019 -0.4694867
## P11554_217 -0.1521109 -0.4018938 -0.2533602 -0.2363987 -0.4332461 -0.5923283
## P11554_218 -0.4942792 -0.4635115 -0.2375526 -0.2294486 -0.4691402 -0.4595016
## P11554_225 -0.4054307 -0.3896783 -0.5804708 -0.3814603 -0.5245094 -0.5032799
## P11554_226 -0.9593661 -0.6829076 -0.5961183 -0.7129492 -0.3471433 -0.4996717
## P11554_227 -0.8593822 -0.6794022 -0.6958409 -0.7772118 -0.4302694 -0.4836665
## P11554_228 -1.1262522 -0.8900384 -1.3551797 -1.2098105 -0.9683017 -1.0880630
## P11554_229 -1.3961275 -1.1564622 -1.0342415 -1.0802694 -1.1133669 -1.0551579
## P11554_230 -0.8856078 -1.2041202 -1.2236903 -1.0780506 -1.3623365 -0.9866664
## AT4G21100 AT5G16750 AT5G62440 AT4G32720 AT5G38110 AT1G59760
## P11554_207 1.1009617 1.0002691 1.1855783 1.1434216 1.2332156 0.8927473
## P11554_208 1.0616974 1.1233640 1.2231847 1.3277204 1.0933375 0.9607755
## P11554_209 1.1892801 1.0899307 1.2195419 1.1467105 1.4594556 0.9144042
## P11554_210 -0.6806545 -0.4804685 -0.6328770 -0.6074427 -0.6858124 -0.9672855
## P11554_211 -0.5930692 -0.6461171 -0.6039677 -0.5737664 -0.5603448 -0.6710644
## P11554_212 -0.6355299 -0.5433900 -0.6606093 -0.4859506 -0.7769773 -0.4176623
## P11554_213 1.4079178 1.5211086 1.4452430 1.4352732 1.1060374 1.5798527
## P11554_214 1.4482780 1.5641705 1.4081227 1.4452409 1.4858847 1.7063451
## P11554_215 1.7898439 1.6917209 1.6217933 1.6441208 1.6400713 1.7389765
## P11554_216 -0.5885128 -0.5124627 -0.3606747 -0.5423087 -0.6314178 -0.7030201
## P11554_217 -0.7343403 -0.4682845 -0.4772281 -0.5995787 -0.2407016 -0.3876487
## P11554_218 -0.3896834 -0.4422557 -0.5054026 -0.5448706 -0.4664166 -0.3517075
## P11554_225 -0.4253893 -0.4792011 -0.7094360 -0.6585981 -0.7467310 -0.6522212
## P11554_226 -0.6113604 -0.6428803 -0.6825387 -0.7212674 -0.5180344 -0.5694999
## P11554_227 -0.3267121 -0.7040329 -0.5987865 -0.7626961 -0.4715177 -0.4421913
## P11554_228 -1.1151522 -1.0676933 -1.0310631 -0.9579297 -0.9738838 -1.0458788
## P11554_229 -0.9734629 -1.1019759 -0.8533728 -0.8440643 -1.1731618 -1.2331797
## P11554_230 -0.9241119 -0.9018018 -0.9875074 -0.8440141 -0.7730027 -0.3517421
## AT2G38280 AT3G18730 AT1G47870 AT1G01370 AT4G02460 AT3G60830
## P11554_207 1.0172914 1.1104582 1.1979456 1.0774924 1.1040710 1.0154352
## P11554_208 1.2126982 1.3946866 1.3673092 0.9760469 1.1458063 0.9826750
## P11554_209 1.3231821 1.5015212 1.5439056 1.3844050 1.5061699 1.3673070
## P11554_210 -0.6538808 -0.5431913 -0.4304366 -0.2086459 -0.2466275 -0.6658254
## P11554_211 -0.5841784 -0.5149633 -0.6393645 -0.5515003 -0.3151451 -0.8824222
## P11554_212 -0.4789596 -0.2945135 -0.2838209 -0.5661568 -0.2866156 -0.8705249
## P11554_213 1.4613942 1.2776922 1.3609523 1.6468283 1.3806348 1.9621926
## P11554_214 1.4485565 1.3089160 1.2891883 1.1982197 1.3223978 1.0680331
## P11554_215 1.4043052 1.4848328 1.2938822 1.6721586 1.4811517 1.4278835
## P11554_216 -0.8842228 -0.6740330 -0.8668406 -0.5492081 -0.6866920 -0.6499329
## P11554_217 -0.8497017 -0.6116845 -0.6008572 -0.4413494 -0.4625901 -0.5935191
## P11554_218 -0.7758341 -0.6914168 -0.5938030 -0.5609742 -0.5323456 0.1134767
## P11554_225 -0.1657288 -0.5769586 -0.4490311 -0.8324846 -0.9644814 -0.6850750
## P11554_226 -0.1603307 -0.6702442 -0.5134674 -0.9305390 -0.9143301 -0.5374909
## P11554_227 -0.1675804 -0.5087445 -0.6359517 -0.5722250 -0.5973125 -0.5715524
## P11554_228 -1.1401093 -1.0424832 -0.9660095 -1.1861148 -1.2898066 -1.1769980
## P11554_229 -1.1425365 -1.1061925 -1.1612209 -0.6316731 -0.7971661 -0.7429850
## P11554_230 -0.8643645 -0.8436819 -0.9123799 -0.9242798 -0.8471189 -0.5606772
## AT5G13480 AT5G22370 AT5G22130 AT4G15900 AT3G49600
## P11554_207 0.53589180 0.94309924 1.11933107 0.6149923 1.2283031
## P11554_208 0.79146688 0.88799945 1.02068301 1.2306433 1.6137918
## P11554_209 2.06947285 0.97490658 1.25305568 1.3607076 1.5729629
## P11554_210 -0.46248481 -0.26690351 -0.49202963 -0.5563394 -0.9633772
## P11554_211 -0.09030563 -0.44953720 -0.39932985 -0.5448430 -0.3083672
## P11554_212 -0.29697587 -0.28620717 -0.27268512 -0.3716877 -0.3906767
## P11554_213 1.47634527 1.45325835 1.51027069 1.2964098 1.2689877
## P11554_214 0.82349210 1.29752874 1.48281483 1.4323680 1.1408983
## P11554_215 1.22130222 1.60540180 1.22695839 1.4978277 0.8601132
## P11554_216 -0.51355355 -0.15236766 -0.41827897 -0.4518310 -1.0007204
## P11554_217 -0.20151187 0.16612519 -0.55911420 -0.4235795 -0.5860091
## P11554_218 -0.09885862 -0.08574135 -0.67307494 -0.2542934 -0.7900491
## P11554_225 -0.85361755 -0.52549308 -0.46693343 -0.5953220 -0.5666813
## P11554_226 -0.04064397 -0.56773673 -0.08860887 0.0455064 0.4215722
## P11554_227 -0.36262705 -0.60511867 -0.20033974 -0.1928980 -0.7522507
## P11554_228 -1.98622668 -1.65515498 -1.27273720 -1.6385976 -0.9907735
## P11554_229 -1.02437484 -1.63499193 -1.46011447 -1.2935612 -0.9905778
## P11554_230 -0.98679067 -1.09906706 -1.30986724 -1.1555024 -0.7671463
## AT3G61140 AT4G32010 AT4G11140 AT3G60630 AT4G00310 AT2G38560
## P11554_207 0.86932974 0.5590480 0.8790719 1.3849262 1.09065942 1.5026279
## P11554_208 1.19502555 1.4523791 -0.5763852 0.7883268 0.92267389 1.1192749
## P11554_209 1.42514622 1.5577850 -0.5763852 0.4605700 0.29559469 0.2572377
## P11554_210 -1.03828715 -1.1701386 -0.5763852 -0.4061729 -0.55795013 -0.6167697
## P11554_211 -0.84195229 -0.6786439 -0.5763852 -0.4032363 -1.19586459 -0.9442658
## P11554_212 -0.72392117 -0.6277934 -0.5763852 -0.7037834 -0.56710283 -0.7135531
## P11554_213 1.42368342 1.3126475 2.2689178 1.3349224 1.83866279 1.8433457
## P11554_214 1.27561224 1.4621463 1.5562792 1.5488488 1.06269802 1.6504905
## P11554_215 1.51643168 1.2466520 1.8686306 0.9653812 1.76194068 1.2738432
## P11554_216 -0.90887905 -0.9411770 -0.5763852 0.3235036 -0.13301420 -0.4735182
## P11554_217 -0.32633345 -0.8318101 0.9201088 0.3579746 -0.39945081 -0.6570428
## P11554_218 -0.69405124 -0.6409034 -0.5763852 -0.5225392 0.01059674 -0.3260785
## P11554_225 -0.06463421 -0.1910948 -0.5763852 0.7429130 0.52186609 -0.0461024
## P11554_226 0.10425120 -0.2892703 -0.5763852 -1.0240739 -0.67212091 -0.6887886
## P11554_227 -0.26340724 0.1982398 -0.5763852 -1.1978093 -1.46476875 -0.8356106
## P11554_228 -1.16988796 -1.1821572 -0.5763852 -0.7548691 -0.78209707 -0.6048684
## P11554_229 -0.69889119 -0.2992072 -0.5763852 -1.3720894 -0.99874758 -1.0702835
## P11554_230 -1.07923510 -0.9367019 -0.5763852 -1.5227930 -0.73357545 -0.6699381
## AT1G66740 AT3G49240 AT1G10270 AT1G57820 AT4G31160
## P11554_207 1.2608632 1.189994e+00 0.941882536 0.3595012 0.5300181
## P11554_208 1.3817413 1.047152e+00 1.277041760 0.9980755 1.2717835
## P11554_209 0.3009029 8.334214e-01 0.846721551 1.3659949 1.0656650
## P11554_210 -0.9326347 -4.128209e-01 -0.002343113 -0.7097144 -0.8738082
## P11554_211 -0.7907723 -2.417889e-01 0.082127117 -0.7075302 -0.2494166
## P11554_212 -0.4160252 -2.527077e-01 0.187705681 -0.4287885 -0.2713102
## P11554_213 1.4745948 1.609544e+00 1.182477528 1.3732173 1.7603126
## P11554_214 1.5376138 1.400800e+00 1.477589338 1.5306195 1.8437133
## P11554_215 1.5624647 1.443258e+00 1.176205593 1.2481212 1.1984330
## P11554_216 -0.9159843 3.185032e-05 -0.117196103 -0.2094874 -0.5308218
## P11554_217 -0.7147934 -1.893314e-02 0.121545791 0.2428382 -0.2358867
## P11554_218 -0.7883952 -2.147730e-01 0.037528982 0.4524641 -0.5649845
## P11554_225 0.1001368 -1.140138e+00 -1.062484309 -1.7248064 -0.8457845
## P11554_226 -0.9500095 -1.112568e+00 -1.248272484 -0.9743803 -1.1179412
## P11554_227 -0.3482732 -1.093439e+00 -1.093486798 -1.3859117 -1.1145662
## P11554_228 -0.2495576 -9.715734e-01 -1.318684819 -0.8391944 -0.7134727
## P11554_229 -0.2306910 -1.093349e+00 -1.316764446 -0.2596083 -0.7949240
## P11554_230 -1.2811810 -9.721111e-01 -1.171593807 -0.3314103 -0.3570088
## AT1G71830 AT1G55350 AT4G32880 AT3G24650 AT5G09810 AT3G10220
## P11554_207 0.21461865 0.3981399 -0.03883533 -0.3425598 -1.03737321 -1.1071672
## P11554_208 0.29668321 0.7696070 0.16069296 -0.3425598 -0.63618019 -0.4150851
## P11554_209 0.11507326 1.0460612 -0.06216564 -0.3425598 -0.15134967 -1.7127357
## P11554_210 0.06344933 -0.9759153 -0.29835789 -0.3425598 -1.44998203 -1.0175325
## P11554_211 0.08600105 -0.7706494 -0.54969984 -0.3425598 -1.48464756 -1.1452617
## P11554_212 -0.21202354 -0.5640309 -1.02409776 -0.3425598 -1.49138287 -0.4971921
## P11554_213 1.75866680 1.4071312 1.28854703 2.5146476 0.73715036 0.5103835
## P11554_214 1.25516385 1.4432899 0.47354274 -0.3425598 0.55036730 0.2896028
## P11554_215 1.76694588 1.2792771 0.24770215 -0.3425598 0.19409483 1.3587569
## P11554_216 0.63340361 0.4382059 -1.25987043 -0.3425598 0.40676596 -0.9218281
## P11554_217 0.39160787 0.8949184 -1.77872157 -0.3425598 0.58110490 -1.0586191
## P11554_218 0.39975571 0.5648357 -0.98526659 -0.3425598 0.89776719 0.3855977
## P11554_225 -0.92656710 -0.7338903 2.02358996 2.9663094 0.64590475 0.4654619
## P11554_226 -0.49881481 -0.9906513 1.19333973 -0.3425598 1.76030562 1.5142233
## P11554_227 -1.27897573 -0.7686354 1.32374553 -0.3425598 1.43463422 1.1810544
## P11554_228 -1.31417138 -0.9084687 -0.71944537 -0.3425598 -1.08996838 0.2837827
## P11554_229 -1.51294268 -1.5332359 -0.18724557 -0.3425598 0.04004043 0.9460597
## P11554_230 -1.23787396 -0.9959890 0.19254589 -0.3425598 0.09274835 0.9404988
## AT3G21510 AT1G55180 AT2G28350 AT1G69670 AT2G45160
## P11554_207 -1.33722137 -0.2357023 -1.03047732 -1.13844310 -0.7241674
## P11554_208 0.08451992 -0.2357023 -1.40731993 -0.76663111 -0.7624029
## P11554_209 0.22005695 -0.2357023 -1.47446048 -0.17376929 -0.5436184
## P11554_210 0.74729385 -0.2357023 -0.02819102 1.09229077 0.5720496
## P11554_211 0.76411028 -0.2357023 0.02762297 0.82201372 0.6151379
## P11554_212 0.01940049 -0.2357023 -0.73529811 0.79300194 0.3622695
## P11554_213 -1.33722137 -0.2357023 -0.35203606 -1.09264478 -1.4818147
## P11554_214 0.01116223 -0.2357023 -0.85795100 -1.46055381 -0.7894277
## P11554_215 0.04563998 -0.2357023 -0.28165257 -2.13927409 -1.1219562
## P11554_216 -1.33722137 -0.2357023 0.46245940 0.01181905 0.9302269
## P11554_217 -1.33722137 -0.2357023 -0.06854129 -0.24486940 -0.3465013
## P11554_218 -0.05535010 -0.2357023 -0.98409451 -0.08097323 -0.6303630
## P11554_225 -1.33722137 -0.2357023 1.88290471 0.61904418 0.5939082
## P11554_226 0.06212751 -0.2357023 1.47826030 0.54683380 -0.4042964
## P11554_227 1.41131419 -0.2357023 0.63033331 0.10637691 -0.9601606
## P11554_228 1.76192662 -0.2357023 1.46306425 1.72290413 1.9540213
## P11554_229 0.33089119 -0.2357023 0.76655264 0.69221312 1.7553891
## P11554_230 1.28301372 4.0069384 0.50882469 0.69066119 0.9817063
## AT2G43790 AT3G09840 AT3G27670 AT2G26890 AT3G51810
## P11554_207 -1.642028520 -1.26017568 -1.35978327 -1.7662982 -0.89936221
## P11554_208 -1.378239200 -0.94529898 -1.00959461 -0.8876377 -0.89936221
## P11554_209 -0.767815776 -0.71804161 -1.26017940 -0.6906474 -0.89936221
## P11554_210 -0.017636797 0.28892589 0.72644963 0.4075192 -0.89936221
## P11554_211 -0.011344501 0.24666024 0.85645467 0.6365053 0.37210560
## P11554_212 0.207746079 0.37005714 0.78897425 1.0158025 0.84137152
## P11554_213 -1.220594481 -1.46151894 -1.27818416 -1.6717685 -0.89936221
## P11554_214 -1.075147238 -1.29519877 -0.93241475 -0.9003710 -0.89936221
## P11554_215 -1.210697824 -1.61393530 -1.68881132 -1.5948855 -0.89936221
## P11554_216 0.211249286 0.01874048 0.12375581 0.6694764 -0.89936221
## P11554_217 0.432490405 0.21481830 0.15563697 0.6462947 -0.89936221
## P11554_218 0.008000941 0.31283516 0.06929903 0.1053888 0.05049825
## P11554_225 0.654679979 0.42313858 0.32173692 0.5415800 1.28374443
## P11554_226 1.227081442 0.52074281 0.13993830 0.7739583 0.89616913
## P11554_227 0.869037797 0.54832615 0.79759081 1.1816594 1.13728947
## P11554_228 0.949608743 1.19096278 1.16798405 -0.2234032 0.42704056
## P11554_229 1.287856721 1.57973631 0.80199293 0.6500261 1.24079898
## P11554_230 1.475752943 1.57922543 1.57915413 1.1068008 1.84524196
## AT5G46210 AT5G60410 AT5G20490 AT1G50030 AT3G08850 AT3G12400
## P11554_207 -1.43773457 -1.7224402 -1.7279927 -1.57146041 -1.3513721 -1.31674179
## P11554_208 -0.71147110 -1.3380981 -1.4455369 -1.03500289 -0.9888080 -1.15081918
## P11554_209 -0.81933305 -0.4263909 -1.2208266 -0.77757380 -1.3908492 -1.45510761
## P11554_210 0.17242829 0.3838773 0.5099163 0.37821970 0.8149700 1.10879402
## P11554_211 0.15090207 -0.2377363 0.5664035 0.61741333 0.8674527 1.27136720
## P11554_212 0.76376656 0.2671240 0.7821475 0.90970487 1.0245027 0.46921208
## P11554_213 -0.69326984 -1.0146178 -0.9684897 -1.58017706 -0.9819609 -0.96664716
## P11554_214 -1.41013147 -1.0815673 -0.8823615 -1.10470153 -1.2771934 -1.15079954
## P11554_215 -0.67010863 -0.3549440 -0.8927406 -1.26359068 -1.0811242 -1.24056602
## P11554_216 -0.18742470 -0.7733691 0.9468482 0.93681239 0.6947820 1.19407342
## P11554_217 -0.33467546 0.5214622 1.1570398 1.04446139 0.5498794 1.27300797
## P11554_218 -0.29586220 -0.3605248 1.0731112 0.61271433 0.2983558 0.75450925
## P11554_225 0.01660766 0.1017572 -0.3642273 -0.03548032 -0.2427112 -0.48437398
## P11554_226 0.42536309 0.4062798 -0.2843946 -0.45186476 -0.5601705 -0.09247390
## P11554_227 0.13533536 0.9106027 -0.2021416 0.07053477 -0.1215778 0.08978476
## P11554_228 0.55480342 1.5149320 1.0333877 1.11075512 1.0273757 0.46067841
## P11554_229 2.30850627 1.4812144 0.6633695 0.83237482 1.2618455 0.86062530
## P11554_230 2.03229831 1.7224388 1.2564880 1.30686074 1.4566035 0.37547678
## AT1G17580 AT4G02570
## P11554_207 -2.316724466 -1.83677238
## P11554_208 -0.519997736 -0.37036370
## P11554_209 -0.759644880 0.35794509
## P11554_210 0.173325847 0.31933947
## P11554_211 0.470355678 0.41802093
## P11554_212 0.980310992 1.23360801
## P11554_213 -1.199715425 -1.45096384
## P11554_214 0.003077474 -1.09285308
## P11554_215 -0.841447762 -0.65610279
## P11554_216 0.168941182 0.51634266
## P11554_217 0.359879450 0.56889672
## P11554_218 0.555484511 1.38379798
## P11554_225 -0.198144829 -1.73009069
## P11554_226 -0.623235407 0.29499499
## P11554_227 -0.152939586 0.02147920
## P11554_228 0.851545268 -0.08320649
## P11554_229 0.771180110 0.94776470
## P11554_230 2.277749579 1.15816323
##
## $`GO:0051301`$rowDendrogram
## 'dendrogram' with 2 branches and 74 members total, at height 3.824561
##
## $`GO:0051301`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0051301`$breaks
## [1] -4.00693843 -3.92679966 -3.84666089 -3.76652212 -3.68638335 -3.60624458
## [7] -3.52610582 -3.44596705 -3.36582828 -3.28568951 -3.20555074 -3.12541197
## [13] -3.04527320 -2.96513444 -2.88499567 -2.80485690 -2.72471813 -2.64457936
## [19] -2.56444059 -2.48430182 -2.40416306 -2.32402429 -2.24388552 -2.16374675
## [25] -2.08360798 -2.00346921 -1.92333044 -1.84319168 -1.76305291 -1.68291414
## [31] -1.60277537 -1.52263660 -1.44249783 -1.36235907 -1.28222030 -1.20208153
## [37] -1.12194276 -1.04180399 -0.96166522 -0.88152645 -0.80138769 -0.72124892
## [43] -0.64111015 -0.56097138 -0.48083261 -0.40069384 -0.32055507 -0.24041631
## [49] -0.16027754 -0.08013877 0.00000000 0.08013877 0.16027754 0.24041631
## [55] 0.32055507 0.40069384 0.48083261 0.56097138 0.64111015 0.72124892
## [61] 0.80138769 0.88152645 0.96166522 1.04180399 1.12194276 1.20208153
## [67] 1.28222030 1.36235907 1.44249783 1.52263660 1.60277537 1.68291414
## [73] 1.76305291 1.84319168 1.92333044 2.00346921 2.08360798 2.16374675
## [79] 2.24388552 2.32402429 2.40416306 2.48430182 2.56444059 2.64457936
## [85] 2.72471813 2.80485690 2.88499567 2.96513444 3.04527320 3.12541197
## [91] 3.20555074 3.28568951 3.36582828 3.44596705 3.52610582 3.60624458
## [97] 3.68638335 3.76652212 3.84666089 3.92679966 4.00693843
##
## $`GO:0051301`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0051301`$colorTable
## low high color
## 1 -4.00693843 -3.92679966 #0000FF
## 2 -3.92679966 -3.84666089 #0505FF
## 3 -3.84666089 -3.76652212 #0A0AFF
## 4 -3.76652212 -3.68638335 #0F0FFF
## 5 -3.68638335 -3.60624458 #1414FF
## 6 -3.60624458 -3.52610582 #1919FF
## 7 -3.52610582 -3.44596705 #1E1EFF
## 8 -3.44596705 -3.36582828 #2424FF
## 9 -3.36582828 -3.28568951 #2929FF
## 10 -3.28568951 -3.20555074 #2E2EFF
## 11 -3.20555074 -3.12541197 #3333FF
## 12 -3.12541197 -3.04527320 #3838FF
## 13 -3.04527320 -2.96513444 #3D3DFF
## 14 -2.96513444 -2.88499567 #4242FF
## 15 -2.88499567 -2.80485690 #4848FF
## 16 -2.80485690 -2.72471813 #4D4DFF
## 17 -2.72471813 -2.64457936 #5252FF
## 18 -2.64457936 -2.56444059 #5757FF
## 19 -2.56444059 -2.48430182 #5C5CFF
## 20 -2.48430182 -2.40416306 #6161FF
## 21 -2.40416306 -2.32402429 #6767FF
## 22 -2.32402429 -2.24388552 #6C6CFF
## 23 -2.24388552 -2.16374675 #7171FF
## 24 -2.16374675 -2.08360798 #7676FF
## 25 -2.08360798 -2.00346921 #7B7BFF
## 26 -2.00346921 -1.92333044 #8080FF
## 27 -1.92333044 -1.84319168 #8585FF
## 28 -1.84319168 -1.76305291 #8B8BFF
## 29 -1.76305291 -1.68291414 #9090FF
## 30 -1.68291414 -1.60277537 #9595FF
## 31 -1.60277537 -1.52263660 #9A9AFF
## 32 -1.52263660 -1.44249783 #9F9FFF
## 33 -1.44249783 -1.36235907 #A4A4FF
## 34 -1.36235907 -1.28222030 #AAAAFF
## 35 -1.28222030 -1.20208153 #AFAFFF
## 36 -1.20208153 -1.12194276 #B4B4FF
## 37 -1.12194276 -1.04180399 #B9B9FF
## 38 -1.04180399 -0.96166522 #BEBEFF
## 39 -0.96166522 -0.88152645 #C3C3FF
## 40 -0.88152645 -0.80138769 #C8C8FF
## 41 -0.80138769 -0.72124892 #CECEFF
## 42 -0.72124892 -0.64111015 #D3D3FF
## 43 -0.64111015 -0.56097138 #D8D8FF
## 44 -0.56097138 -0.48083261 #DDDDFF
## 45 -0.48083261 -0.40069384 #E2E2FF
## 46 -0.40069384 -0.32055507 #E7E7FF
## 47 -0.32055507 -0.24041631 #ECECFF
## 48 -0.24041631 -0.16027754 #F2F2FF
## 49 -0.16027754 -0.08013877 #F7F7FF
## 50 -0.08013877 0.00000000 #FCFCFF
## 51 0.00000000 0.08013877 #FFFCFC
## 52 0.08013877 0.16027754 #FFF7F7
## 53 0.16027754 0.24041631 #FFF2F2
## 54 0.24041631 0.32055507 #FFECEC
## 55 0.32055507 0.40069384 #FFE7E7
## 56 0.40069384 0.48083261 #FFE2E2
## 57 0.48083261 0.56097138 #FFDDDD
## 58 0.56097138 0.64111015 #FFD8D8
## 59 0.64111015 0.72124892 #FFD3D3
## 60 0.72124892 0.80138769 #FFCECE
## 61 0.80138769 0.88152645 #FFC8C8
## 62 0.88152645 0.96166522 #FFC3C3
## 63 0.96166522 1.04180399 #FFBEBE
## 64 1.04180399 1.12194276 #FFB9B9
## 65 1.12194276 1.20208153 #FFB4B4
## 66 1.20208153 1.28222030 #FFAFAF
## 67 1.28222030 1.36235907 #FFA9A9
## 68 1.36235907 1.44249783 #FFA4A4
## 69 1.44249783 1.52263660 #FF9F9F
## 70 1.52263660 1.60277537 #FF9A9A
## 71 1.60277537 1.68291414 #FF9595
## 72 1.68291414 1.76305291 #FF9090
## 73 1.76305291 1.84319168 #FF8B8B
## 74 1.84319168 1.92333044 #FF8585
## 75 1.92333044 2.00346921 #FF8080
## 76 2.00346921 2.08360798 #FF7B7B
## 77 2.08360798 2.16374675 #FF7676
## 78 2.16374675 2.24388552 #FF7171
## 79 2.24388552 2.32402429 #FF6C6C
## 80 2.32402429 2.40416306 #FF6767
## 81 2.40416306 2.48430182 #FF6161
## 82 2.48430182 2.56444059 #FF5C5C
## 83 2.56444059 2.64457936 #FF5757
## 84 2.64457936 2.72471813 #FF5252
## 85 2.72471813 2.80485690 #FF4D4D
## 86 2.80485690 2.88499567 #FF4848
## 87 2.88499567 2.96513444 #FF4242
## 88 2.96513444 3.04527320 #FF3D3D
## 89 3.04527320 3.12541197 #FF3838
## 90 3.12541197 3.20555074 #FF3333
## 91 3.20555074 3.28568951 #FF2E2E
## 92 3.28568951 3.36582828 #FF2929
## 93 3.36582828 3.44596705 #FF2424
## 94 3.44596705 3.52610582 #FF1E1E
## 95 3.52610582 3.60624458 #FF1919
## 96 3.60624458 3.68638335 #FF1414
## 97 3.68638335 3.76652212 #FF0F0F
## 98 3.76652212 3.84666089 #FF0A0A
## 99 3.84666089 3.92679966 #FF0505
## 100 3.92679966 4.00693843 #FF0000
##
## $`GO:0051301`$layout
## $`GO:0051301`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0051301`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0051301`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0007267`
## $`GO:0007267`$rowInd
## [1] 32 65 54 62 44 48 61 9 49 35 40 47 41 4 14 68 50 5 29 13 2 23 33 21 24
## [26] 80 77 52 10 45 75 7 20 72 30 15 66 78 22 70 25 38 57 79 73 71 36 27 37 6
## [51] 26 11 67 63 8 58 17 64 43 60 34 46 42 12 18 3 1 55 51 69 39 76 19 74 59
## [76] 56 16 31 53 28
##
## $`GO:0007267`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0007267`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0007267`$carpet
## AT2G31320 AT4G20910 AT3G60740 AT4G13950 AT3G16570 AT3G24340
## P11554_207 0.6746070 0.2286444 0.3625955 0.14409413 0.8195648 1.1675162
## P11554_208 0.7602131 0.9364704 1.0187156 0.82870040 1.0071569 1.0595894
## P11554_209 1.4915479 0.7384526 1.3197268 0.60173582 0.5956243 -0.1304834
## P11554_210 -1.7181133 -1.1259642 -0.9446227 -0.91892647 -0.9785436 -0.6868862
## P11554_211 -0.5416318 -0.6422914 -1.1135566 -0.93234417 -0.7939924 0.2596507
## P11554_212 -0.2930092 -0.5604655 -0.2542039 -1.32500925 -1.2584199 0.5041160
## P11554_213 2.0062609 1.2835512 0.5266130 -0.01348407 0.3421364 0.9357344
## P11554_214 0.9813375 0.7781553 0.4465593 0.39388985 0.4486510 0.4900528
## P11554_215 1.1176996 0.9060881 0.4421321 0.25130068 0.0877192 0.7741082
## P11554_216 -1.6263809 -1.6546271 -1.3489987 -0.42761550 -0.6746407 0.2910721
## P11554_217 -0.4775084 -1.4122696 -0.9891169 -0.81764221 -0.7464342 -1.8138943
## P11554_218 -0.9091896 -1.4278292 -0.5555976 -0.73049843 -1.2361606 -0.1168626
## P11554_225 -0.2039350 0.8962905 0.9590563 2.22960990 1.6106571 0.4384562
## P11554_226 -0.1909670 0.9466315 1.4552357 1.44944686 1.4129988 1.0144006
## P11554_227 0.0143302 0.9394540 1.4528621 1.44866569 1.5147696 0.2873560
## P11554_228 -0.3172102 0.4817486 -1.2997539 -0.56255455 -0.1762088 -0.8461378
## P11554_229 -0.3936088 -0.7306285 -1.0418753 -0.63759883 -1.1528501 -1.8138943
## P11554_230 -0.3744421 -0.5814111 -0.4357708 -0.98176984 -0.8220279 -1.8138943
## AT4G12970 AT1G23147 AT3G25170 AT2G33130 AT3G04735 AT3G23805
## P11554_207 -0.2357023 2.6528377 -0.2357023 -0.343577 -0.2357023 0.248820580
## P11554_208 4.0069384 -0.4296998 -0.2357023 -0.343577 -0.2357023 0.336926186
## P11554_209 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -1.012402991
## P11554_210 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -1.071170873
## P11554_211 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -1.117526664
## P11554_212 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -1.750210623
## P11554_213 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 1.205236032
## P11554_214 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 1.617577307
## P11554_215 -0.2357023 -0.4296998 -0.2357023 -0.343577 4.0069384 1.734575645
## P11554_216 -0.2357023 1.8777752 -0.2357023 -0.343577 -0.2357023 0.748884489
## P11554_217 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -0.582103801
## P11554_218 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 0.003700231
## P11554_225 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 0.823986177
## P11554_226 -0.2357023 1.9148846 4.0069384 2.776016 -0.2357023 0.607707679
## P11554_227 -0.2357023 -0.4296998 -0.2357023 2.721216 -0.2357023 0.142658003
## P11554_228 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -0.792707491
## P11554_229 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -0.646810575
## P11554_230 -0.2357023 -0.4296998 -0.2357023 -0.343577 -0.2357023 -0.497139310
## AT3G05490 AT1G13220 AT1G48410 AT4G32551 AT3G28730 AT1G14690
## P11554_207 -0.5697022 0.2237902 -1.52185850 -0.24586246 -0.13054870 0.1659207
## P11554_208 -0.3459588 0.4242057 0.05451137 -0.02343463 0.19426429 1.1852905
## P11554_209 -0.7734944 -0.5970388 0.29427536 1.24411664 1.06469143 0.9232878
## P11554_210 -0.3583740 -0.2763459 -1.20210992 -1.44750996 -0.55302107 -0.2433289
## P11554_211 -0.6200579 -0.5645592 -1.01390535 -0.96563300 -0.77290097 -0.2492209
## P11554_212 -0.9016876 -0.9125255 -0.17301048 -1.40266329 0.52339236 -0.2134631
## P11554_213 1.3590096 1.7436094 0.48140777 0.55744855 1.15459167 0.9463752
## P11554_214 1.7292348 1.6056486 0.93994463 -0.33049464 0.42138809 1.1691222
## P11554_215 1.9205177 1.9126058 0.46290840 1.41713729 1.57421692 0.5451309
## P11554_216 0.9924449 0.8413009 0.73776929 0.60384180 -1.59885563 0.8784796
## P11554_217 0.9792312 -0.2281249 1.72800670 -0.35985219 -0.16269951 1.0294652
## P11554_218 0.6875802 0.5902724 1.12843318 0.75311016 0.01480992 1.0213956
## P11554_225 -0.3064405 -0.4577976 -1.93815311 -1.04945055 -1.77644692 -0.9828624
## P11554_226 -0.7251219 -0.6996219 -0.82091856 1.10591582 -0.26071494 -1.1338511
## P11554_227 -0.3058800 -0.9876139 0.47505566 0.96265526 -0.90377567 -1.2826664
## P11554_228 -0.8734185 -0.5523965 -0.70839668 -1.78357653 -0.66735898 -1.8212926
## P11554_229 -0.4796253 -1.6194727 0.20531390 0.41395223 -0.01222251 -1.0745297
## P11554_230 -1.4082571 -0.4459360 0.87072635 0.55029948 1.89119023 -0.8632526
## AT2G25420 AT1G34355 AT1G02900 AT1G72970 AT2G31970
## P11554_207 0.53170106 0.24804861 0.42872359 1.19550158 0.51952604
## P11554_208 0.95277411 0.41249520 -0.05431102 0.32431449 1.30550584
## P11554_209 0.63944597 -0.01991303 0.12455107 -0.01369041 0.80285990
## P11554_210 0.28796548 0.64174815 -0.34224203 0.97357155 0.21256270
## P11554_211 -0.02887163 0.48999551 -0.24271767 1.27102720 0.56207816
## P11554_212 -0.21990657 0.92099743 -0.35183374 -0.51475806 1.20296068
## P11554_213 0.68556765 0.95520235 0.73315926 1.40134628 0.98678503
## P11554_214 1.00023712 0.45922760 0.36631416 0.99313853 0.95922779
## P11554_215 1.67351025 0.69784078 1.95440748 1.20005183 0.70916466
## P11554_216 0.25101189 1.36247064 0.33591095 0.47499530 0.05033542
## P11554_217 0.30041623 0.91982736 1.59375858 -0.75317440 -0.17523484
## P11554_218 1.01704981 0.69497838 1.30443338 -0.44955327 0.39014806
## P11554_225 -0.56720161 -1.05633582 -1.18390541 -0.45837801 -1.75119982
## P11554_226 -1.37275710 -1.72969005 -1.93497142 -1.07728135 -1.48056476
## P11554_227 -0.76376557 -1.32848374 -0.44951498 -1.28696075 -0.79919408
## P11554_228 -1.51796106 -1.35965654 -1.37623412 -1.32062972 -1.12394590
## P11554_229 -0.88696620 -0.94739114 -0.46319748 -0.45012203 -1.28324758
## P11554_230 -1.98224981 -1.36136171 -0.44233061 -1.50939877 -1.08776731
## AT1G63640 AT1G77720 AT5G67070 AT5G35930 AT3G49250
## P11554_207 0.65362148 0.97425879 0.348571889 -0.2550288 0.76182230
## P11554_208 1.19793097 1.05826600 0.191294594 0.7420486 1.00506220
## P11554_209 0.66940459 0.89830918 0.225627566 0.1649827 0.76986399
## P11554_210 0.03018073 0.04140483 -0.819493573 -0.5239356 -0.61754522
## P11554_211 0.11017199 -0.34322660 -0.868044891 -1.2774198 0.26859315
## P11554_212 0.41654947 0.33677735 -0.631480842 0.1016979 -0.37966898
## P11554_213 1.36595007 1.26326310 1.835577361 1.4210169 1.28148975
## P11554_214 1.35216418 1.59378183 1.671862472 1.7256504 1.75177795
## P11554_215 1.42003958 1.43112268 1.797836059 1.8317097 1.31526822
## P11554_216 -0.05780029 -0.35255970 0.002588406 -0.7111505 0.08304583
## P11554_217 -0.33709362 -0.10433074 -0.039844939 -0.2101764 0.16784242
## P11554_218 0.21448053 -0.31364149 0.278038670 0.6562950 -0.10292561
## P11554_225 -1.16443712 -1.23652945 -0.035520663 -0.5701578 -1.34319574
## P11554_226 -1.22178465 -1.52393831 0.076992215 0.2070990 -0.62472957
## P11554_227 -1.55998944 -0.93248433 -0.120625268 0.3823568 -0.37228891
## P11554_228 -1.35670972 -0.94605323 -1.046239074 -1.2112736 -1.10646208
## P11554_229 -0.81421892 -0.64249945 -1.797556125 -1.4192289 -1.21526705
## P11554_230 -0.91845984 -1.20192046 -1.069583857 -1.0544858 -1.64268264
## AT1G26540 AT3G20010 AT5G23880 AT1G18450 AT1G63470
## P11554_207 0.69773232 0.93889288 0.68316039 0.1997885 0.39827854
## P11554_208 0.93587684 0.94266435 0.91042166 1.1631874 0.72631587
## P11554_209 0.95170879 1.37792033 1.23114395 1.0523593 0.78423093
## P11554_210 -0.47804100 -0.35428011 -0.23667702 -0.7738995 -0.89809460
## P11554_211 -0.48181082 -0.21429687 -0.29782419 -0.6016317 -0.86570646
## P11554_212 -0.53452334 -0.40798317 -0.36563397 -0.1509401 -0.23404125
## P11554_213 1.53455025 1.23990884 1.33242798 1.1999075 1.12779060
## P11554_214 1.72236590 1.53968926 1.39493209 1.2799718 1.45144030
## P11554_215 1.76972728 1.44631677 1.65436121 1.6818944 2.39794751
## P11554_216 -0.24555133 -0.57974628 0.01999552 0.5098118 -0.05419263
## P11554_217 -0.10911501 -0.02996640 -0.22163234 0.1455423 -0.08785984
## P11554_218 -0.08775657 -0.04288418 0.18706582 0.2071693 -0.13224827
## P11554_225 -0.77071186 -0.33274296 -0.95454343 -1.1496693 -0.60672659
## P11554_226 -1.03938844 -0.79236854 -0.56847034 -0.5946507 0.15292517
## P11554_227 -0.83160183 -0.77997065 -0.73913757 -0.3888784 -0.92178326
## P11554_228 -1.06499628 -1.39070806 -1.56691396 -1.9368146 -1.38938201
## P11554_229 -1.06913676 -1.49895895 -1.00835940 -0.9873295 -0.76576286
## P11554_230 -0.89932815 -1.06148626 -1.45431639 -0.8558186 -1.08313112
## AT5G13000 AT2G27040 AT1G52310 AT4G30130 AT5G43810
## P11554_207 0.5290992 0.41763475 0.3347911 1.2209651 1.078106753
## P11554_208 0.8678384 0.80432846 1.1593615 2.0888481 1.293367617
## P11554_209 0.8735574 0.97810208 0.1920263 0.3744631 1.637428463
## P11554_210 -0.8245061 -0.80293132 -0.6373051 0.0916218 -0.571227883
## P11554_211 -0.7016047 -0.64779678 -0.2159094 1.0670679 -0.044726623
## P11554_212 -0.5782164 -0.42616786 -0.5807162 -0.3091093 0.442939512
## P11554_213 1.5463975 1.79610316 1.0279786 0.8988833 0.482358113
## P11554_214 1.8885572 1.49547662 0.9177961 0.6269807 1.275407582
## P11554_215 1.7481533 1.67298644 1.4121368 0.6989575 0.265311577
## P11554_216 -0.2840557 -0.33735093 1.0206551 -0.9671433 -0.688008688
## P11554_217 -0.2159659 0.24673487 1.2563267 -0.1352951 -0.046085440
## P11554_218 -0.3538349 -0.07633598 -0.1787383 -1.0619098 -0.660969030
## P11554_225 -0.6692221 -0.57290586 -1.7476072 -0.5487987 -0.738120266
## P11554_226 -0.2589288 -0.37937398 -0.2840614 -1.1106923 0.559766566
## P11554_227 -0.2697694 -0.36750535 -0.1504639 0.5247837 -0.002159109
## P11554_228 -1.1359227 -1.17399648 -1.7000081 -1.2891476 -2.283075403
## P11554_229 -1.4099146 -1.09200549 -1.3909118 -1.3721170 -0.848652249
## P11554_230 -0.7516615 -1.53499634 -0.4353509 -0.7983579 -1.151661491
## AT1G67720 AT5G02520 AT1G79950 AT2G47230 AT4G02460 AT5G63960
## P11554_207 2.26994666 1.3095250 1.0202117 1.1782779 1.1040710 1.1713245
## P11554_208 1.08273076 1.3714185 1.3262327 1.2746736 1.1458063 1.4549063
## P11554_209 0.85686673 1.3639613 1.2747931 1.1717015 1.5061699 1.2718754
## P11554_210 -0.38813020 -0.5063147 -0.5933934 -0.6616361 -0.2466275 -0.4380328
## P11554_211 -0.66990641 -0.3262023 -0.6227158 -0.5155419 -0.3151451 -0.3767061
## P11554_212 -0.70269383 -0.1291863 -0.2619343 -0.4668954 -0.2866156 -0.1143842
## P11554_213 1.07719461 1.1536365 1.4788413 1.5551862 1.3806348 1.3679954
## P11554_214 0.90913832 1.1323069 1.4565954 1.4495981 1.3223978 1.3458729
## P11554_215 0.32330415 1.5778187 1.3275226 1.4838396 1.4811517 1.3777394
## P11554_216 -0.53274518 -0.5578037 -0.4289616 -0.4404988 -0.6866920 -0.7198209
## P11554_217 -0.04633694 -0.3368507 -0.5091918 -0.6088417 -0.4625901 -0.6517789
## P11554_218 -0.89249312 -0.8315809 -0.6039719 -0.6391131 -0.5323456 -0.5775556
## P11554_225 -0.09210698 -0.8509071 -0.5086952 -0.7398462 -0.9644814 -0.8001198
## P11554_226 0.66491493 -0.6355880 -0.6626215 -0.6015085 -0.9143301 -0.7574147
## P11554_227 -0.42442069 -0.5099174 -0.1849924 -0.5664692 -0.5973125 -0.4070590
## P11554_228 -1.69863481 -0.9570335 -1.0423317 -0.8885405 -1.2898066 -1.1241694
## P11554_229 -1.43825937 -1.3228988 -1.1100756 -1.0595206 -0.7971661 -1.0238247
## P11554_230 -0.29836864 -0.9443836 -1.3553116 -0.9248649 -0.8471189 -0.9988476
## AT5G13960 AT5G07660 AT2G39810 AT2G04660 AT2G41500 AT1G15940
## P11554_207 1.0043766 1.2489549 1.0190973 1.07739255 0.05371391 0.66447219
## P11554_208 1.3085413 1.5530785 1.0574856 1.20933328 0.63243545 1.09904282
## P11554_209 1.4788660 1.0678267 1.3057022 0.97961431 1.37934650 1.25457761
## P11554_210 -0.5948637 -0.5562306 -0.9499288 -0.52168925 -1.04871269 -0.48621910
## P11554_211 -0.3661511 -0.5788684 -0.7452699 -0.14361329 -0.73102220 -0.63116509
## P11554_212 -0.2414945 -0.3248160 -0.4641232 -0.29296701 -0.60359012 -0.15017172
## P11554_213 1.4390728 1.5205099 1.4202017 1.86541622 1.97365889 1.53815073
## P11554_214 1.2730129 1.1882190 1.3839114 1.23090727 1.59371631 1.70173669
## P11554_215 1.2866363 1.5131207 1.5140591 1.09795206 1.48405688 1.33385521
## P11554_216 -0.4534059 -0.7627030 -0.9580326 -0.57384071 -0.23238575 -0.67153976
## P11554_217 -0.4221551 -0.8524258 -0.7126134 -0.67491146 -0.44776873 -0.30835143
## P11554_218 -0.1337019 -0.6409672 -0.7614616 -0.89260216 -0.61728952 -0.35735464
## P11554_225 -0.8574390 -0.8694127 0.1506114 -0.28921836 0.04505351 -1.36329774
## P11554_226 -0.7709018 -0.4358695 -0.2219320 -0.11901983 -0.25208271 -1.08610872
## P11554_227 -0.3838525 -0.7069094 0.0375305 -0.06899327 -0.46384018 -1.17670938
## P11554_228 -1.3729869 -1.0280267 -0.9523112 -1.20870403 -1.25230610 -0.61176411
## P11554_229 -0.9757506 -0.7422745 -1.0881668 -1.57735310 -1.21976551 -0.77881942
## P11554_230 -1.2178030 -0.5932058 -1.0347599 -1.09770322 -0.29321794 0.02966586
## AT1G80070 AT1G28270 AT4G30520 AT4G14010 AT1G23145 AT4G02680
## P11554_207 -0.01727095 -1.1203284 -1.23792720 0.05533561 -0.6660491 -1.3308708
## P11554_208 1.01597205 1.3615340 0.19192144 -0.29840188 -0.6660491 -0.6491262
## P11554_209 1.60394095 -1.1203284 0.11025213 -0.18371571 -0.6660491 -0.4068994
## P11554_210 -0.57861865 -1.1203284 0.67224206 -0.25403005 -0.6660491 -0.5736486
## P11554_211 -0.60856498 0.6094841 1.67392327 0.79361513 -0.6660491 0.3698936
## P11554_212 0.14364166 -1.1203284 1.29726468 0.12178932 -0.6660491 0.2498876
## P11554_213 0.99648996 -1.1203284 -0.69066438 -1.50142413 -0.6660491 0.6474680
## P11554_214 1.82558364 0.2389941 0.72838307 -1.50142413 1.0496459 0.3597557
## P11554_215 1.29034482 0.8509567 -0.66149251 0.52479243 -0.6660491 1.1507537
## P11554_216 -0.48663979 1.2838196 0.14370403 1.57951215 1.0863126 1.0755470
## P11554_217 0.04434975 0.2282866 0.45689574 0.45874245 1.7409211 2.0377186
## P11554_218 -0.54038401 0.1719422 0.31787870 0.03236878 -0.6660491 0.8150792
## P11554_225 -1.03205865 0.5950864 -0.34597774 0.53443422 -0.6660491 -0.2395097
## P11554_226 -0.65672229 0.2903729 -0.75856714 -1.50142413 1.1144946 -1.6982802
## P11554_227 -0.35059283 1.6505050 1.48977335 1.09847739 -0.6660491 -1.6565144
## P11554_228 -1.86238034 -1.1203284 -1.35248031 -1.50142413 0.9446569 -0.3695215
## P11554_229 -1.00591506 0.5613169 -0.04506474 -0.08993208 -0.6660491 -0.3498109
## P11554_230 0.21882473 -1.1203284 -1.99006447 1.63270874 2.0565580 0.5680783
## AT1G59750 AT4G15800 AT3G14980 AT4G11510 AT2G32835 AT3G20550
## P11554_207 -1.87160109 -1.1441945 -0.75328798 -0.7613177 -0.4235532 -0.02832461
## P11554_208 -1.14276650 -1.7336564 -2.16952776 -0.7613177 -0.4235532 -0.19259560
## P11554_209 -1.11498420 -1.3176481 -0.64747997 -0.7613177 -0.4235532 0.18075744
## P11554_210 -1.07266336 0.2595927 -0.01768062 -0.7613177 -0.4235532 -2.08959079
## P11554_211 0.06430631 0.3124882 -0.02735611 -0.7613177 -0.4235532 0.10138744
## P11554_212 0.04093614 -0.2486275 -0.64207184 -0.7613177 -0.4235532 0.63839748
## P11554_213 1.25555904 0.3036502 0.08949454 1.5413474 -0.4235532 -1.47144133
## P11554_214 1.09188571 0.2649745 0.31484866 -0.7613177 -0.4235532 -1.05537712
## P11554_215 -0.62100893 0.7539593 0.03564527 -0.7613177 -0.4235532 -1.20715201
## P11554_216 1.17491283 1.6015125 1.64156328 -0.7613177 -0.4235532 -0.76730071
## P11554_217 1.73855466 1.6911603 1.68991240 -0.7613177 -0.4235532 -0.16309407
## P11554_218 1.32372677 1.5642912 1.87706075 1.2476238 -0.4235532 0.08426137
## P11554_225 0.34176729 -1.0389906 0.10943006 1.1245610 -0.4235532 0.67714673
## P11554_226 -0.32714803 -0.7009261 -0.39282264 0.7895675 -0.4235532 1.01441648
## P11554_227 -0.37352043 -0.7094689 -0.51441630 -0.7613177 2.3469110 0.94431463
## P11554_228 -0.26520763 0.1115789 0.58210573 1.6681699 1.3805054 0.77491213
## P11554_229 -0.02416369 0.1424487 -0.94147392 1.0874358 -0.4235532 0.76397012
## P11554_230 -0.21858489 -0.1121445 -0.23394353 0.9157893 2.6258815 1.79531244
## AT3G12550 AT1G32490 AT1G60860 AT1G10180 AT1G01040 AT3G61670
## P11554_207 -1.0572717 -1.0337991 -1.76418508 -1.07632503 -1.3115320 -1.5364060
## P11554_208 -0.2535475 -0.8426726 1.04476694 -1.65230820 -0.7744384 -0.9949497
## P11554_209 -0.6577436 -0.6610084 -1.04317608 -0.34094014 -1.4200139 -0.8775983
## P11554_210 -0.4421620 -0.5020562 -1.52609755 -0.70708499 0.8988952 0.9084578
## P11554_211 -0.7315885 -0.2281090 -0.80043708 0.79520028 0.7108268 1.2840130
## P11554_212 -0.1804889 0.4718843 0.04036054 1.46892388 0.6246917 1.3714980
## P11554_213 -0.5999747 -1.1902859 0.44329222 0.72878349 -1.2056908 -1.0765944
## P11554_214 -0.8573593 -1.4969458 0.24602003 0.20677914 -0.9238791 -1.1662484
## P11554_215 -0.7444723 -0.4244520 -0.51819749 -0.60893544 -0.9053433 -1.4403948
## P11554_216 -0.7790644 -0.7056244 -1.12831809 -0.11407172 0.7386751 1.0058127
## P11554_217 -1.0206630 -0.4977627 -0.63820830 -0.10497805 1.0933438 1.1213435
## P11554_218 -0.5888197 0.2255402 -0.23912672 0.72420135 1.1233242 0.9985261
## P11554_225 1.6501093 0.7981651 0.65532742 -2.04041059 -0.2724168 -0.1966739
## P11554_226 1.1370248 1.1794312 1.44164004 -0.48839423 -1.0592288 -0.0233746
## P11554_227 1.6514643 0.9984364 1.41305039 0.92970882 -0.1929106 -0.2175078
## P11554_228 0.9361267 1.0630809 0.74612759 -0.02270164 1.0072603 -0.1596830
## P11554_229 1.0083383 0.5811784 0.60332578 1.53492525 0.2873480 0.3378818
## P11554_230 1.5300921 2.2649995 1.02383544 0.76762782 1.5810886 0.6618980
## AT3G43920 AT5G02030 AT3G03300 AT5G25475 AT1G63020 AT5G20320
## P11554_207 -1.64727307 -0.6329378 -1.1671235 -1.6756594 -1.3923576 -1.4692329
## P11554_208 -0.91117855 -0.6179165 -1.2653635 -1.3156358 -1.0181246 -0.9562479
## P11554_209 -0.42900811 -0.3524780 -0.6917712 -1.5989665 -0.7121019 -0.9028566
## P11554_210 0.61625960 1.1595349 1.1788081 0.9298602 0.6103624 0.6202526
## P11554_211 1.07774021 1.3132091 0.4654904 -0.0113235 0.2657725 0.6407808
## P11554_212 1.04526891 1.1799659 1.3258134 0.6815380 0.5926986 1.0292892
## P11554_213 -1.66881669 -1.8140522 -1.9548990 -0.1574369 -1.5725624 -0.9746916
## P11554_214 -0.83540882 -1.6393306 -0.9409194 -1.4671597 -1.4162399 -1.4842077
## P11554_215 -1.38626714 -1.4745319 -0.8944204 -0.5528083 -1.6297587 -1.9204813
## P11554_216 0.86854066 0.8264781 1.0162407 0.9437296 0.2112635 0.0283223
## P11554_217 1.58115735 0.7574347 0.7773962 0.6885873 0.2894457 0.4515604
## P11554_218 0.90555754 0.5978811 0.5489988 1.5370129 0.2331141 0.2723480
## P11554_225 -0.12680717 -0.2084781 -0.7304137 -0.6195375 0.8787729 0.2929101
## P11554_226 -0.17036943 -0.4786688 0.3056770 0.1498166 0.8898291 0.5427557
## P11554_227 -0.30558078 -0.5550081 -0.2577524 0.6026779 1.1645799 0.8616291
## P11554_228 -0.02024755 0.5059021 0.3922378 0.5309910 0.5338681 0.7763242
## P11554_229 0.57803997 0.7481412 0.7098016 1.1273434 1.2014328 1.1669007
## P11554_230 0.82839307 0.6848550 1.1821991 0.2069706 0.8700056 1.0246448
## AT4G11130 AT4G02020 AT1G54490 AT2G28290 AT3G57300
## P11554_207 -1.20817116 -1.14609778 -1.54786562 -1.598407729 -1.49453637
## P11554_208 -0.29313899 -0.47259664 -1.19977274 -0.897973326 -1.00256764
## P11554_209 -0.80268859 -0.50897021 -0.60761995 -0.729718839 -1.45820264
## P11554_210 0.26695250 0.78813996 0.47977619 -0.225498472 -0.17884559
## P11554_211 0.59170956 0.64923294 0.70415571 0.009059281 0.06271207
## P11554_212 1.09483597 1.30865112 1.02374449 0.652195899 0.80173130
## P11554_213 -1.60393167 -1.20049158 -1.46135676 -1.303445640 -1.29449428
## P11554_214 -1.22732848 -1.74610465 -0.94449463 -0.739814054 -0.68609147
## P11554_215 -1.92313413 -1.97235879 -0.97350789 -1.362540984 -1.22687775
## P11554_216 0.07155204 -0.10222851 -0.19211720 0.114598826 -0.05185905
## P11554_217 -0.01775822 0.22610203 0.06983100 0.600958661 0.22925493
## P11554_218 -0.22752745 -0.03638426 0.23425133 0.324075474 0.54040959
## P11554_225 0.46684278 0.31851912 -0.33571819 -0.064865493 0.16559213
## P11554_226 0.71905725 0.10888412 0.05210359 0.108255228 0.60186398
## P11554_227 0.54404742 0.63964037 0.43097040 0.685340782 1.14351103
## P11554_228 1.34182452 1.19356631 1.13749573 0.948210616 1.08578207
## P11554_229 1.31423443 0.70011703 1.08784197 1.187784646 1.01731193
## P11554_230 0.89262221 1.25237943 2.04228257 2.291785125 1.74530575
## AT2G16390
## P11554_207 -1.7937118
## P11554_208 -0.5709286
## P11554_209 -0.9449207
## P11554_210 0.4052434
## P11554_211 1.0841476
## P11554_212 0.4029780
## P11554_213 -1.4020702
## P11554_214 -1.3283511
## P11554_215 -0.9859428
## P11554_216 -0.5137124
## P11554_217 0.7448645
## P11554_218 0.8953971
## P11554_225 0.7447231
## P11554_226 0.5487191
## P11554_227 -0.2891289
## P11554_228 1.2543943
## P11554_229 0.2834583
## P11554_230 1.4648410
##
## $`GO:0007267`$rowDendrogram
## 'dendrogram' with 2 branches and 80 members total, at height 3.839715
##
## $`GO:0007267`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0007267`$breaks
## [1] -4.00693843 -3.92679966 -3.84666089 -3.76652212 -3.68638335 -3.60624458
## [7] -3.52610582 -3.44596705 -3.36582828 -3.28568951 -3.20555074 -3.12541197
## [13] -3.04527320 -2.96513444 -2.88499567 -2.80485690 -2.72471813 -2.64457936
## [19] -2.56444059 -2.48430182 -2.40416306 -2.32402429 -2.24388552 -2.16374675
## [25] -2.08360798 -2.00346921 -1.92333044 -1.84319168 -1.76305291 -1.68291414
## [31] -1.60277537 -1.52263660 -1.44249783 -1.36235907 -1.28222030 -1.20208153
## [37] -1.12194276 -1.04180399 -0.96166522 -0.88152645 -0.80138769 -0.72124892
## [43] -0.64111015 -0.56097138 -0.48083261 -0.40069384 -0.32055507 -0.24041631
## [49] -0.16027754 -0.08013877 0.00000000 0.08013877 0.16027754 0.24041631
## [55] 0.32055507 0.40069384 0.48083261 0.56097138 0.64111015 0.72124892
## [61] 0.80138769 0.88152645 0.96166522 1.04180399 1.12194276 1.20208153
## [67] 1.28222030 1.36235907 1.44249783 1.52263660 1.60277537 1.68291414
## [73] 1.76305291 1.84319168 1.92333044 2.00346921 2.08360798 2.16374675
## [79] 2.24388552 2.32402429 2.40416306 2.48430182 2.56444059 2.64457936
## [85] 2.72471813 2.80485690 2.88499567 2.96513444 3.04527320 3.12541197
## [91] 3.20555074 3.28568951 3.36582828 3.44596705 3.52610582 3.60624458
## [97] 3.68638335 3.76652212 3.84666089 3.92679966 4.00693843
##
## $`GO:0007267`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0007267`$colorTable
## low high color
## 1 -4.00693843 -3.92679966 #0000FF
## 2 -3.92679966 -3.84666089 #0505FF
## 3 -3.84666089 -3.76652212 #0A0AFF
## 4 -3.76652212 -3.68638335 #0F0FFF
## 5 -3.68638335 -3.60624458 #1414FF
## 6 -3.60624458 -3.52610582 #1919FF
## 7 -3.52610582 -3.44596705 #1E1EFF
## 8 -3.44596705 -3.36582828 #2424FF
## 9 -3.36582828 -3.28568951 #2929FF
## 10 -3.28568951 -3.20555074 #2E2EFF
## 11 -3.20555074 -3.12541197 #3333FF
## 12 -3.12541197 -3.04527320 #3838FF
## 13 -3.04527320 -2.96513444 #3D3DFF
## 14 -2.96513444 -2.88499567 #4242FF
## 15 -2.88499567 -2.80485690 #4848FF
## 16 -2.80485690 -2.72471813 #4D4DFF
## 17 -2.72471813 -2.64457936 #5252FF
## 18 -2.64457936 -2.56444059 #5757FF
## 19 -2.56444059 -2.48430182 #5C5CFF
## 20 -2.48430182 -2.40416306 #6161FF
## 21 -2.40416306 -2.32402429 #6767FF
## 22 -2.32402429 -2.24388552 #6C6CFF
## 23 -2.24388552 -2.16374675 #7171FF
## 24 -2.16374675 -2.08360798 #7676FF
## 25 -2.08360798 -2.00346921 #7B7BFF
## 26 -2.00346921 -1.92333044 #8080FF
## 27 -1.92333044 -1.84319168 #8585FF
## 28 -1.84319168 -1.76305291 #8B8BFF
## 29 -1.76305291 -1.68291414 #9090FF
## 30 -1.68291414 -1.60277537 #9595FF
## 31 -1.60277537 -1.52263660 #9A9AFF
## 32 -1.52263660 -1.44249783 #9F9FFF
## 33 -1.44249783 -1.36235907 #A4A4FF
## 34 -1.36235907 -1.28222030 #AAAAFF
## 35 -1.28222030 -1.20208153 #AFAFFF
## 36 -1.20208153 -1.12194276 #B4B4FF
## 37 -1.12194276 -1.04180399 #B9B9FF
## 38 -1.04180399 -0.96166522 #BEBEFF
## 39 -0.96166522 -0.88152645 #C3C3FF
## 40 -0.88152645 -0.80138769 #C8C8FF
## 41 -0.80138769 -0.72124892 #CECEFF
## 42 -0.72124892 -0.64111015 #D3D3FF
## 43 -0.64111015 -0.56097138 #D8D8FF
## 44 -0.56097138 -0.48083261 #DDDDFF
## 45 -0.48083261 -0.40069384 #E2E2FF
## 46 -0.40069384 -0.32055507 #E7E7FF
## 47 -0.32055507 -0.24041631 #ECECFF
## 48 -0.24041631 -0.16027754 #F2F2FF
## 49 -0.16027754 -0.08013877 #F7F7FF
## 50 -0.08013877 0.00000000 #FCFCFF
## 51 0.00000000 0.08013877 #FFFCFC
## 52 0.08013877 0.16027754 #FFF7F7
## 53 0.16027754 0.24041631 #FFF2F2
## 54 0.24041631 0.32055507 #FFECEC
## 55 0.32055507 0.40069384 #FFE7E7
## 56 0.40069384 0.48083261 #FFE2E2
## 57 0.48083261 0.56097138 #FFDDDD
## 58 0.56097138 0.64111015 #FFD8D8
## 59 0.64111015 0.72124892 #FFD3D3
## 60 0.72124892 0.80138769 #FFCECE
## 61 0.80138769 0.88152645 #FFC8C8
## 62 0.88152645 0.96166522 #FFC3C3
## 63 0.96166522 1.04180399 #FFBEBE
## 64 1.04180399 1.12194276 #FFB9B9
## 65 1.12194276 1.20208153 #FFB4B4
## 66 1.20208153 1.28222030 #FFAFAF
## 67 1.28222030 1.36235907 #FFA9A9
## 68 1.36235907 1.44249783 #FFA4A4
## 69 1.44249783 1.52263660 #FF9F9F
## 70 1.52263660 1.60277537 #FF9A9A
## 71 1.60277537 1.68291414 #FF9595
## 72 1.68291414 1.76305291 #FF9090
## 73 1.76305291 1.84319168 #FF8B8B
## 74 1.84319168 1.92333044 #FF8585
## 75 1.92333044 2.00346921 #FF8080
## 76 2.00346921 2.08360798 #FF7B7B
## 77 2.08360798 2.16374675 #FF7676
## 78 2.16374675 2.24388552 #FF7171
## 79 2.24388552 2.32402429 #FF6C6C
## 80 2.32402429 2.40416306 #FF6767
## 81 2.40416306 2.48430182 #FF6161
## 82 2.48430182 2.56444059 #FF5C5C
## 83 2.56444059 2.64457936 #FF5757
## 84 2.64457936 2.72471813 #FF5252
## 85 2.72471813 2.80485690 #FF4D4D
## 86 2.80485690 2.88499567 #FF4848
## 87 2.88499567 2.96513444 #FF4242
## 88 2.96513444 3.04527320 #FF3D3D
## 89 3.04527320 3.12541197 #FF3838
## 90 3.12541197 3.20555074 #FF3333
## 91 3.20555074 3.28568951 #FF2E2E
## 92 3.28568951 3.36582828 #FF2929
## 93 3.36582828 3.44596705 #FF2424
## 94 3.44596705 3.52610582 #FF1E1E
## 95 3.52610582 3.60624458 #FF1919
## 96 3.60624458 3.68638335 #FF1414
## 97 3.68638335 3.76652212 #FF0F0F
## 98 3.76652212 3.84666089 #FF0A0A
## 99 3.84666089 3.92679966 #FF0505
## 100 3.92679966 4.00693843 #FF0000
##
## $`GO:0007267`$layout
## $`GO:0007267`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0007267`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0007267`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0007017`
## $`GO:0007017`$rowInd
## [1] 17 14 9 16 21 6 13 1 20 8 18 2 4 7 3 19 15 5 12 11 10
##
## $`GO:0007017`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0007017`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0007017`$carpet
## AT5G12250 AT3G60740 AT2G35630 AT4G38950 AT5G48120
## P11554_207 1.01310448 0.3625955 0.1430261 0.61678989 0.927973362
## P11554_208 1.07728782 1.0187156 1.2003548 0.83278006 1.232566658
## P11554_209 1.74123425 1.3197268 0.6027948 1.36542957 1.457262303
## P11554_210 -0.22340226 -0.9446227 -1.1445314 -1.24378513 -0.634402768
## P11554_211 -0.05105366 -1.1135566 -0.8213790 -0.73763707 -0.284745361
## P11554_212 -0.15911724 -0.2542039 -0.5580962 -0.87837989 -0.591787979
## P11554_213 0.62819604 0.5266130 1.4564536 1.80827289 1.277558766
## P11554_214 0.94442155 0.4465593 1.8962345 1.45694180 1.072097161
## P11554_215 0.34820451 0.4421321 1.8502377 1.54499981 1.695682054
## P11554_216 -0.23399446 -1.3489987 -0.4144303 -0.05644639 -1.295595007
## P11554_217 -0.51877346 -0.9891169 -0.4645613 -0.58683798 -1.163376914
## P11554_218 -0.14546970 -0.5555976 -0.3899318 -0.73404987 -0.631159181
## P11554_225 -0.22207016 0.9590563 -0.4330152 -0.40960257 -0.785943232
## P11554_226 0.45539693 1.4552357 0.0371837 -0.14343372 -0.004303675
## P11554_227 0.40784419 1.4528621 -0.1109510 -0.36832104 0.028160499
## P11554_228 -2.43063000 -1.2997539 -1.1600034 -1.05341650 -0.902797509
## P11554_229 -1.03457418 -1.0418753 -1.1804531 -0.48234020 -0.986153867
## P11554_230 -1.59660466 -0.4357708 -0.5089325 -0.93096368 -0.411035314
## AT2G07170 AT3G57060 AT1G04820 AT5G23860 AT2G29550 AT5G19780
## P11554_207 1.16246877 0.9055023 0.3439908 0.3794242 0.1310512 0.3597171
## P11554_208 1.21521868 1.3248193 0.3992504 0.3432332 0.5708164 0.5490231
## P11554_209 1.21044060 1.2934175 0.4477707 0.5813971 0.7295304 0.6998046
## P11554_210 -0.66107760 -1.1210399 -0.6573452 -0.6536335 -0.7481668 -0.8258303
## P11554_211 -0.12282299 -0.3383086 -0.5259092 -0.5370360 -0.6784380 -0.6229056
## P11554_212 0.10803380 -0.1828023 -0.6861032 -0.7629816 -0.7691975 -0.8137399
## P11554_213 0.86065807 1.1779512 1.6479346 1.7189540 1.3343424 1.3895713
## P11554_214 1.47539009 1.7583214 1.7452839 1.7402803 1.6689398 1.5966033
## P11554_215 1.28567065 1.3730028 1.6742281 1.6000069 1.3170253 1.4907055
## P11554_216 -0.12647254 -0.9483376 0.5340004 0.3325845 0.6921219 0.6400695
## P11554_217 0.05602871 -0.1049427 0.4259223 0.3219671 0.7092924 0.6639006
## P11554_218 0.23599004 -0.5949872 0.4370309 0.3417132 0.7355537 0.5802608
## P11554_225 -1.08364674 -0.9290415 -0.7866537 -0.6710811 -0.6632016 -0.7295494
## P11554_226 -1.05232203 -0.7377822 -0.6266267 -0.3193042 -0.5748630 -0.5207351
## P11554_227 -1.13010657 -0.3559859 -0.6479091 -0.4295104 -0.4049358 -0.5089175
## P11554_228 -1.31162882 -0.9782933 -1.1997151 -1.3969466 -1.7149547 -1.6745996
## P11554_229 -1.24453093 -0.6305703 -1.0875526 -0.9878590 -0.9573779 -1.0773214
## P11554_230 -0.87729120 -0.9109230 -1.4375972 -1.6012080 -1.3775382 -1.1960571
## AT1G20010 AT1G50010 AT2G16960 AT1G23220 AT5G20110
## P11554_207 -0.01621384 0.5212103 0.7507300 -0.2313748 1.499764822
## P11554_208 0.15191099 0.5108780 0.2208699 0.6325258 0.615923003
## P11554_209 0.33565806 0.5196580 0.7572320 -0.3447339 0.169777905
## P11554_210 -0.81376750 -0.3956559 -0.1357354 -0.2074379 -1.363573565
## P11554_211 -0.71522624 -0.2533151 0.1263280 0.3899693 0.705472112
## P11554_212 -0.78642917 -0.5212547 0.8231631 1.6384612 1.307037129
## P11554_213 2.12449051 1.5085726 0.9788360 -0.1036907 -1.363573565
## P11554_214 1.89614734 1.5690105 0.4685176 -1.8915740 -0.035907254
## P11554_215 1.69347453 1.4904491 0.4421712 -0.3853606 -0.001959232
## P11554_216 0.07336438 0.6467112 1.2764184 -1.4456979 -1.363573565
## P11554_217 0.19750907 0.5674713 0.9886698 0.2919081 -0.046365419
## P11554_218 0.38793521 0.4246418 1.0017659 -0.1936652 1.457548933
## P11554_225 -0.41068444 -0.9400601 -1.2183806 -0.8145368 -1.363573565
## P11554_226 -0.45958671 -1.0765168 -1.2391764 -1.0745170 0.014274977
## P11554_227 -0.57921079 -0.9456320 -1.6126028 1.9807346 -0.009928913
## P11554_228 -0.96339097 -0.6757951 -1.4082173 -0.1537870 0.398952286
## P11554_229 -1.15287121 -1.2759311 -1.2680410 0.9149520 -1.363573565
## P11554_230 -0.96310921 -1.6744422 -0.9525483 0.9978245 0.743277476
## AT4G15930 AT1G64740 AT3G44200 AT3G16120 AT2G40730
## P11554_207 -1.75778025 -1.4735795 -1.3808606 -0.6650381 -2.96390603
## P11554_208 -1.69998416 -0.9793049 -1.1584601 -0.6650381 -0.77346157
## P11554_209 -1.18667540 -0.7892601 -0.8106267 1.2279407 0.15965364
## P11554_210 0.30117569 0.6477472 0.8489747 -0.6650381 -0.91593793
## P11554_211 -0.30803022 0.3964392 1.0436602 -0.6650381 -0.57073463
## P11554_212 0.24518634 0.5728144 1.2973551 2.1905559 0.51906288
## P11554_213 -0.85691659 -1.2854393 -1.5118129 -0.6650381 0.59355407
## P11554_214 -1.34159437 -1.4441564 -1.2193226 -0.6650381 0.33759844
## P11554_215 -0.39773970 -1.5797635 -1.0400561 -0.6650381 -0.27958572
## P11554_216 0.65066899 0.6993732 0.7539289 1.0090436 -0.18556597
## P11554_217 0.31150303 0.7384874 0.8060383 -0.6650381 0.26809029
## P11554_218 1.38024615 0.7407431 1.0893873 -0.6650381 -0.85226046
## P11554_225 0.88608121 -0.2168095 -0.4325019 -0.6650381 0.80488927
## P11554_226 0.97615339 0.3114415 -0.2556676 1.0359666 1.45089943
## P11554_227 1.00772118 0.1669480 -0.3683096 1.0060860 1.03489030
## P11554_228 0.06392309 0.7846254 0.8609064 1.5108649 0.47367036
## P11554_229 0.88801317 1.5368152 0.4922013 -0.6650381 0.04474284
## P11554_230 0.83804846 1.1728784 0.9851659 -0.6650381 0.85440078
##
## $`GO:0007017`$rowDendrogram
## 'dendrogram' with 2 branches and 21 members total, at height 1.984466
##
## $`GO:0007017`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0007017`$breaks
## [1] -2.96390603 -2.90462791 -2.84534979 -2.78607166 -2.72679354 -2.66751542
## [7] -2.60823730 -2.54895918 -2.48968106 -2.43040294 -2.37112482 -2.31184670
## [13] -2.25256858 -2.19329046 -2.13401234 -2.07473422 -2.01545610 -1.95617798
## [19] -1.89689986 -1.83762174 -1.77834362 -1.71906550 -1.65978737 -1.60050925
## [25] -1.54123113 -1.48195301 -1.42267489 -1.36339677 -1.30411865 -1.24484053
## [31] -1.18556241 -1.12628429 -1.06700617 -1.00772805 -0.94844993 -0.88917181
## [37] -0.82989369 -0.77061557 -0.71133745 -0.65205933 -0.59278121 -0.53350308
## [43] -0.47422496 -0.41494684 -0.35566872 -0.29639060 -0.23711248 -0.17783436
## [49] -0.11855624 -0.05927812 0.00000000 0.05927812 0.11855624 0.17783436
## [55] 0.23711248 0.29639060 0.35566872 0.41494684 0.47422496 0.53350308
## [61] 0.59278121 0.65205933 0.71133745 0.77061557 0.82989369 0.88917181
## [67] 0.94844993 1.00772805 1.06700617 1.12628429 1.18556241 1.24484053
## [73] 1.30411865 1.36339677 1.42267489 1.48195301 1.54123113 1.60050925
## [79] 1.65978737 1.71906550 1.77834362 1.83762174 1.89689986 1.95617798
## [85] 2.01545610 2.07473422 2.13401234 2.19329046 2.25256858 2.31184670
## [91] 2.37112482 2.43040294 2.48968106 2.54895918 2.60823730 2.66751542
## [97] 2.72679354 2.78607166 2.84534979 2.90462791 2.96390603
##
## $`GO:0007017`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0007017`$colorTable
## low high color
## 1 -2.96390603 -2.90462791 #0000FF
## 2 -2.90462791 -2.84534979 #0505FF
## 3 -2.84534979 -2.78607166 #0A0AFF
## 4 -2.78607166 -2.72679354 #0F0FFF
## 5 -2.72679354 -2.66751542 #1414FF
## 6 -2.66751542 -2.60823730 #1919FF
## 7 -2.60823730 -2.54895918 #1E1EFF
## 8 -2.54895918 -2.48968106 #2424FF
## 9 -2.48968106 -2.43040294 #2929FF
## 10 -2.43040294 -2.37112482 #2E2EFF
## 11 -2.37112482 -2.31184670 #3333FF
## 12 -2.31184670 -2.25256858 #3838FF
## 13 -2.25256858 -2.19329046 #3D3DFF
## 14 -2.19329046 -2.13401234 #4242FF
## 15 -2.13401234 -2.07473422 #4848FF
## 16 -2.07473422 -2.01545610 #4D4DFF
## 17 -2.01545610 -1.95617798 #5252FF
## 18 -1.95617798 -1.89689986 #5757FF
## 19 -1.89689986 -1.83762174 #5C5CFF
## 20 -1.83762174 -1.77834362 #6161FF
## 21 -1.77834362 -1.71906550 #6767FF
## 22 -1.71906550 -1.65978737 #6C6CFF
## 23 -1.65978737 -1.60050925 #7171FF
## 24 -1.60050925 -1.54123113 #7676FF
## 25 -1.54123113 -1.48195301 #7B7BFF
## 26 -1.48195301 -1.42267489 #8080FF
## 27 -1.42267489 -1.36339677 #8585FF
## 28 -1.36339677 -1.30411865 #8B8BFF
## 29 -1.30411865 -1.24484053 #9090FF
## 30 -1.24484053 -1.18556241 #9595FF
## 31 -1.18556241 -1.12628429 #9A9AFF
## 32 -1.12628429 -1.06700617 #9F9FFF
## 33 -1.06700617 -1.00772805 #A4A4FF
## 34 -1.00772805 -0.94844993 #AAAAFF
## 35 -0.94844993 -0.88917181 #AFAFFF
## 36 -0.88917181 -0.82989369 #B4B4FF
## 37 -0.82989369 -0.77061557 #B9B9FF
## 38 -0.77061557 -0.71133745 #BEBEFF
## 39 -0.71133745 -0.65205933 #C3C3FF
## 40 -0.65205933 -0.59278121 #C8C8FF
## 41 -0.59278121 -0.53350308 #CECEFF
## 42 -0.53350308 -0.47422496 #D3D3FF
## 43 -0.47422496 -0.41494684 #D8D8FF
## 44 -0.41494684 -0.35566872 #DDDDFF
## 45 -0.35566872 -0.29639060 #E2E2FF
## 46 -0.29639060 -0.23711248 #E7E7FF
## 47 -0.23711248 -0.17783436 #ECECFF
## 48 -0.17783436 -0.11855624 #F2F2FF
## 49 -0.11855624 -0.05927812 #F7F7FF
## 50 -0.05927812 0.00000000 #FCFCFF
## 51 0.00000000 0.05927812 #FFFCFC
## 52 0.05927812 0.11855624 #FFF7F7
## 53 0.11855624 0.17783436 #FFF2F2
## 54 0.17783436 0.23711248 #FFECEC
## 55 0.23711248 0.29639060 #FFE7E7
## 56 0.29639060 0.35566872 #FFE2E2
## 57 0.35566872 0.41494684 #FFDDDD
## 58 0.41494684 0.47422496 #FFD8D8
## 59 0.47422496 0.53350308 #FFD3D3
## 60 0.53350308 0.59278121 #FFCECE
## 61 0.59278121 0.65205933 #FFC8C8
## 62 0.65205933 0.71133745 #FFC3C3
## 63 0.71133745 0.77061557 #FFBEBE
## 64 0.77061557 0.82989369 #FFB9B9
## 65 0.82989369 0.88917181 #FFB4B4
## 66 0.88917181 0.94844993 #FFAFAF
## 67 0.94844993 1.00772805 #FFA9A9
## 68 1.00772805 1.06700617 #FFA4A4
## 69 1.06700617 1.12628429 #FF9F9F
## 70 1.12628429 1.18556241 #FF9A9A
## 71 1.18556241 1.24484053 #FF9595
## 72 1.24484053 1.30411865 #FF9090
## 73 1.30411865 1.36339677 #FF8B8B
## 74 1.36339677 1.42267489 #FF8585
## 75 1.42267489 1.48195301 #FF8080
## 76 1.48195301 1.54123113 #FF7B7B
## 77 1.54123113 1.60050925 #FF7676
## 78 1.60050925 1.65978737 #FF7171
## 79 1.65978737 1.71906550 #FF6C6C
## 80 1.71906550 1.77834362 #FF6767
## 81 1.77834362 1.83762174 #FF6161
## 82 1.83762174 1.89689986 #FF5C5C
## 83 1.89689986 1.95617798 #FF5757
## 84 1.95617798 2.01545610 #FF5252
## 85 2.01545610 2.07473422 #FF4D4D
## 86 2.07473422 2.13401234 #FF4848
## 87 2.13401234 2.19329046 #FF4242
## 88 2.19329046 2.25256858 #FF3D3D
## 89 2.25256858 2.31184670 #FF3838
## 90 2.31184670 2.37112482 #FF3333
## 91 2.37112482 2.43040294 #FF2E2E
## 92 2.43040294 2.48968106 #FF2929
## 93 2.48968106 2.54895918 #FF2424
## 94 2.54895918 2.60823730 #FF1E1E
## 95 2.60823730 2.66751542 #FF1919
## 96 2.66751542 2.72679354 #FF1414
## 97 2.72679354 2.78607166 #FF0F0F
## 98 2.78607166 2.84534979 #FF0A0A
## 99 2.84534979 2.90462791 #FF0505
## 100 2.90462791 2.96390603 #FF0000
##
## $`GO:0007017`$layout
## $`GO:0007017`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0007017`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0007017`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0040029`
## $`GO:0040029`$rowInd
## [1] 15 13 7 8 1 10 14 5 6 2 12 11 9 3 16 4
##
## $`GO:0040029`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0040029`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0040029`$carpet
## AT4G24680 AT4G13520 AT2G33290 AT2G33610 AT1G21700
## P11554_207 -1.3338652 -1.15305181 -0.2318041 -1.01014314 -1.69448212
## P11554_208 0.1148197 -0.32203614 -0.1709910 -1.15162864 -1.63937576
## P11554_209 0.7019795 -0.32606644 -0.0697298 0.07262426 -0.76212646
## P11554_210 -0.7712075 -0.45998475 -0.8836632 -0.95632623 0.04545705
## P11554_211 -0.7983743 -0.33953929 -1.0621427 -1.21305539 -0.03943629
## P11554_212 1.4439755 -0.70956695 -1.0682378 -0.49936206 1.52519342
## P11554_213 -0.3627378 -0.82044097 -0.4141906 0.10395548 -0.30324298
## P11554_214 0.6009217 -0.67218157 -0.1996269 -0.16601942 -0.54550476
## P11554_215 -1.0060776 -0.62897504 0.1696977 0.22666028 -0.13042670
## P11554_216 -0.9191117 -0.66510534 -1.2286028 -0.75593622 0.32736075
## P11554_217 -0.7976451 -0.38630189 -1.2468601 -0.69624509 1.36831255
## P11554_218 -1.0636705 -0.55550285 -0.9097607 -0.38368235 0.82956607
## P11554_225 0.7457063 1.03440723 1.8093692 1.65373582 -0.58792335
## P11554_226 0.7217992 2.18403381 0.9913130 2.19601391 -1.39700313
## P11554_227 1.4982480 2.13977462 1.2807324 1.14285646 0.17120883
## P11554_228 -0.2674902 -0.02083546 1.5576186 0.97744469 0.89885585
## P11554_229 -0.4311000 0.43659602 0.8619424 0.86014130 0.49114158
## P11554_230 1.9238302 1.26477682 0.8149363 -0.40103366 1.44242545
## AT2G46020 AT4G16280 AT2G24740 AT2G28290 AT1G54490
## P11554_207 -2.11482087 -1.60609279 -0.89283517 -1.598407729 -1.54786562
## P11554_208 -0.76055589 -0.64270967 -0.83954206 -0.897973326 -1.19977274
## P11554_209 -0.93105039 -0.40077172 -0.38666930 -0.729718839 -0.60761995
## P11554_210 0.63188861 0.54033742 0.82923747 -0.225498472 0.47977619
## P11554_211 0.64185366 0.02283693 1.31162567 0.009059281 0.70415571
## P11554_212 1.76806713 0.48298831 0.94706688 0.652195899 1.02374449
## P11554_213 -0.57256968 -1.50219360 -1.13824200 -1.303445640 -1.46135676
## P11554_214 -0.19431995 -1.17021464 -1.29534712 -0.739814054 -0.94449463
## P11554_215 -0.73784215 -1.67026148 -1.48696380 -1.362540984 -0.97350789
## P11554_216 1.24563735 0.07095517 -0.46405705 0.114598826 -0.19211720
## P11554_217 1.19634758 -0.22548472 -0.22244273 0.600958661 0.06983100
## P11554_218 1.07591008 -0.21030651 -0.29347854 0.324075474 0.23425133
## P11554_225 -0.66171780 0.78526880 -0.13912917 -0.064865493 -0.33571819
## P11554_226 -0.97023459 1.29736714 -0.06123914 0.108255228 0.05210359
## P11554_227 -0.27560680 1.19113593 -0.25043656 0.685340782 0.43097040
## P11554_228 -0.13964526 0.96416663 1.38409007 0.948210616 1.13749573
## P11554_229 0.01148381 0.97211127 1.57471041 1.187784646 1.08784197
## P11554_230 0.78717517 1.10086753 1.42365215 2.291785125 2.04228257
## AT3G17590 AT2G47620 AT2G35160 AT1G73100 AT5G04940
## P11554_207 -1.2468051 1.21714610 1.69552651 1.06442987 0.6317203
## P11554_208 0.8541754 1.14201626 0.80363708 1.27194929 1.4637083
## P11554_209 0.6562776 0.05301934 1.06842860 0.86260167 1.5834137
## P11554_210 -0.8398321 -0.33839501 -0.12521438 -0.33324870 -0.5006752
## P11554_211 0.5892378 -0.14389833 -0.34248896 0.31421986 -0.4920535
## P11554_212 0.4792745 0.41673316 -0.22351942 0.13791304 -0.2119378
## P11554_213 -1.1185429 1.59438415 1.15862843 1.27219821 1.1539268
## P11554_214 0.3532512 1.40114810 1.28645859 1.51063194 1.5056619
## P11554_215 1.4912575 1.36951604 1.25297147 0.18465356 1.2956360
## P11554_216 0.3019832 -0.33512076 0.02654326 -0.66067776 -0.5957262
## P11554_217 0.1260616 -0.13290120 -0.02932019 -0.39274707 -0.8052234
## P11554_218 0.6264243 -0.24335660 -0.20828993 -1.44670415 -0.9816625
## P11554_225 -1.2047506 -1.67228760 -1.11168565 -0.09829489 0.0151329
## P11554_226 -0.7553896 -0.34426659 -0.46789946 -1.34181677 -0.3701368
## P11554_227 1.1174281 -1.05473299 -0.68250224 0.25267147 -0.4950853
## P11554_228 -1.8954013 -0.98957757 -1.43170905 0.37637412 -0.6760304
## P11554_229 1.2155707 -1.44148562 -1.26794432 -1.15577508 -1.5370676
## P11554_230 -0.7502203 -0.49794089 -1.40162034 -1.81837860 -0.9836013
## AT1G77300
## P11554_207 -0.44392476
## P11554_208 0.82357031
## P11554_209 1.19297684
## P11554_210 -1.06961488
## P11554_211 0.50952611
## P11554_212 0.72323035
## P11554_213 0.58801139
## P11554_214 1.95529664
## P11554_215 1.70356728
## P11554_216 -0.77968835
## P11554_217 -0.93586954
## P11554_218 -1.10964201
## P11554_225 -0.59548791
## P11554_226 -0.58486253
## P11554_227 0.08492790
## P11554_228 0.05250601
## P11554_229 -1.20943891
## P11554_230 -0.90508394
##
## $`GO:0040029`$rowDendrogram
## 'dendrogram' with 2 branches and 16 members total, at height 1.807101
##
## $`GO:0040029`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0040029`$breaks
## [1] -2.2917851 -2.2459494 -2.2001137 -2.1542780 -2.1084423 -2.0626066
## [7] -2.0167709 -1.9709352 -1.9250995 -1.8792638 -1.8334281 -1.7875924
## [13] -1.7417567 -1.6959210 -1.6500853 -1.6042496 -1.5584139 -1.5125782
## [19] -1.4667425 -1.4209068 -1.3750711 -1.3292354 -1.2833997 -1.2375640
## [25] -1.1917283 -1.1458926 -1.1000569 -1.0542212 -1.0083855 -0.9625498
## [31] -0.9167140 -0.8708783 -0.8250426 -0.7792069 -0.7333712 -0.6875355
## [37] -0.6416998 -0.5958641 -0.5500284 -0.5041927 -0.4583570 -0.4125213
## [43] -0.3666856 -0.3208499 -0.2750142 -0.2291785 -0.1833428 -0.1375071
## [49] -0.0916714 -0.0458357 0.0000000 0.0458357 0.0916714 0.1375071
## [55] 0.1833428 0.2291785 0.2750142 0.3208499 0.3666856 0.4125213
## [61] 0.4583570 0.5041927 0.5500284 0.5958641 0.6416998 0.6875355
## [67] 0.7333712 0.7792069 0.8250426 0.8708783 0.9167140 0.9625498
## [73] 1.0083855 1.0542212 1.1000569 1.1458926 1.1917283 1.2375640
## [79] 1.2833997 1.3292354 1.3750711 1.4209068 1.4667425 1.5125782
## [85] 1.5584139 1.6042496 1.6500853 1.6959210 1.7417567 1.7875924
## [91] 1.8334281 1.8792638 1.9250995 1.9709352 2.0167709 2.0626066
## [97] 2.1084423 2.1542780 2.2001137 2.2459494 2.2917851
##
## $`GO:0040029`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0040029`$colorTable
## low high color
## 1 -2.2917851 -2.2459494 #0000FF
## 2 -2.2459494 -2.2001137 #0505FF
## 3 -2.2001137 -2.1542780 #0A0AFF
## 4 -2.1542780 -2.1084423 #0F0FFF
## 5 -2.1084423 -2.0626066 #1414FF
## 6 -2.0626066 -2.0167709 #1919FF
## 7 -2.0167709 -1.9709352 #1E1EFF
## 8 -1.9709352 -1.9250995 #2424FF
## 9 -1.9250995 -1.8792638 #2929FF
## 10 -1.8792638 -1.8334281 #2E2EFF
## 11 -1.8334281 -1.7875924 #3333FF
## 12 -1.7875924 -1.7417567 #3838FF
## 13 -1.7417567 -1.6959210 #3D3DFF
## 14 -1.6959210 -1.6500853 #4242FF
## 15 -1.6500853 -1.6042496 #4848FF
## 16 -1.6042496 -1.5584139 #4D4DFF
## 17 -1.5584139 -1.5125782 #5252FF
## 18 -1.5125782 -1.4667425 #5757FF
## 19 -1.4667425 -1.4209068 #5C5CFF
## 20 -1.4209068 -1.3750711 #6161FF
## 21 -1.3750711 -1.3292354 #6767FF
## 22 -1.3292354 -1.2833997 #6C6CFF
## 23 -1.2833997 -1.2375640 #7171FF
## 24 -1.2375640 -1.1917283 #7676FF
## 25 -1.1917283 -1.1458926 #7B7BFF
## 26 -1.1458926 -1.1000569 #8080FF
## 27 -1.1000569 -1.0542212 #8585FF
## 28 -1.0542212 -1.0083855 #8B8BFF
## 29 -1.0083855 -0.9625498 #9090FF
## 30 -0.9625498 -0.9167140 #9595FF
## 31 -0.9167140 -0.8708783 #9A9AFF
## 32 -0.8708783 -0.8250426 #9F9FFF
## 33 -0.8250426 -0.7792069 #A4A4FF
## 34 -0.7792069 -0.7333712 #AAAAFF
## 35 -0.7333712 -0.6875355 #AFAFFF
## 36 -0.6875355 -0.6416998 #B4B4FF
## 37 -0.6416998 -0.5958641 #B9B9FF
## 38 -0.5958641 -0.5500284 #BEBEFF
## 39 -0.5500284 -0.5041927 #C3C3FF
## 40 -0.5041927 -0.4583570 #C8C8FF
## 41 -0.4583570 -0.4125213 #CECEFF
## 42 -0.4125213 -0.3666856 #D3D3FF
## 43 -0.3666856 -0.3208499 #D8D8FF
## 44 -0.3208499 -0.2750142 #DDDDFF
## 45 -0.2750142 -0.2291785 #E2E2FF
## 46 -0.2291785 -0.1833428 #E7E7FF
## 47 -0.1833428 -0.1375071 #ECECFF
## 48 -0.1375071 -0.0916714 #F2F2FF
## 49 -0.0916714 -0.0458357 #F7F7FF
## 50 -0.0458357 0.0000000 #FCFCFF
## 51 0.0000000 0.0458357 #FFFCFC
## 52 0.0458357 0.0916714 #FFF7F7
## 53 0.0916714 0.1375071 #FFF2F2
## 54 0.1375071 0.1833428 #FFECEC
## 55 0.1833428 0.2291785 #FFE7E7
## 56 0.2291785 0.2750142 #FFE2E2
## 57 0.2750142 0.3208499 #FFDDDD
## 58 0.3208499 0.3666856 #FFD8D8
## 59 0.3666856 0.4125213 #FFD3D3
## 60 0.4125213 0.4583570 #FFCECE
## 61 0.4583570 0.5041927 #FFC8C8
## 62 0.5041927 0.5500284 #FFC3C3
## 63 0.5500284 0.5958641 #FFBEBE
## 64 0.5958641 0.6416998 #FFB9B9
## 65 0.6416998 0.6875355 #FFB4B4
## 66 0.6875355 0.7333712 #FFAFAF
## 67 0.7333712 0.7792069 #FFA9A9
## 68 0.7792069 0.8250426 #FFA4A4
## 69 0.8250426 0.8708783 #FF9F9F
## 70 0.8708783 0.9167140 #FF9A9A
## 71 0.9167140 0.9625498 #FF9595
## 72 0.9625498 1.0083855 #FF9090
## 73 1.0083855 1.0542212 #FF8B8B
## 74 1.0542212 1.1000569 #FF8585
## 75 1.1000569 1.1458926 #FF8080
## 76 1.1458926 1.1917283 #FF7B7B
## 77 1.1917283 1.2375640 #FF7676
## 78 1.2375640 1.2833997 #FF7171
## 79 1.2833997 1.3292354 #FF6C6C
## 80 1.3292354 1.3750711 #FF6767
## 81 1.3750711 1.4209068 #FF6161
## 82 1.4209068 1.4667425 #FF5C5C
## 83 1.4667425 1.5125782 #FF5757
## 84 1.5125782 1.5584139 #FF5252
## 85 1.5584139 1.6042496 #FF4D4D
## 86 1.6042496 1.6500853 #FF4848
## 87 1.6500853 1.6959210 #FF4242
## 88 1.6959210 1.7417567 #FF3D3D
## 89 1.7417567 1.7875924 #FF3838
## 90 1.7875924 1.8334281 #FF3333
## 91 1.8334281 1.8792638 #FF2E2E
## 92 1.8792638 1.9250995 #FF2929
## 93 1.9250995 1.9709352 #FF2424
## 94 1.9709352 2.0167709 #FF1E1E
## 95 2.0167709 2.0626066 #FF1919
## 96 2.0626066 2.1084423 #FF1414
## 97 2.1084423 2.1542780 #FF0F0F
## 98 2.1542780 2.2001137 #FF0A0A
## 99 2.2001137 2.2459494 #FF0505
## 100 2.2459494 2.2917851 #FF0000
##
## $`GO:0040029`$layout
## $`GO:0040029`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0040029`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0040029`$layout$lwid
## [1] 1.5 4.0
##
##
##
## $`GO:0048522`
## $`GO:0048522`$rowInd
## [1] 10 23 16 11 7 5 26 4 6 3 19 13 17 9 1 21 18 25 28 12 14 2 22 8 30
## [26] 24 15 20 29 27 31
##
## $`GO:0048522`$colInd
## [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
##
## $`GO:0048522`$call
## heatmap.2(x = goi2, Colv = FALSE, distfun = pearson.dist, hclustfun = function(X) {
## hclust(X, method = "ward.D2")
## }, dendrogram = "row", col = hpal, trace = "none", margins = c(6,
## 5), labRow = FALSE, labCol = paste(samples$Nutrition, samples$AZD,
## sep = "-")[sel_T6])
##
## $`GO:0048522`$carpet
## AT2G19930 AT4G30870 AT3G07740 AT2G35550 AT1G69600
## P11554_207 -0.71259827 0.32341066 0.5921740 0.16650880 0.4374851
## P11554_208 -0.48033351 -0.20833965 0.0075247 0.52115990 0.3628104
## P11554_209 -0.75353207 0.68961960 -1.7724890 0.15508676 -0.2535749
## P11554_210 1.26007726 0.45888379 0.5392714 0.81336584 0.2933758
## P11554_211 0.91986333 1.00566637 0.6355243 0.20619779 0.9066505
## P11554_212 1.39488401 1.41219409 -0.9696471 1.81688163 0.5467576
## P11554_213 -1.43359813 -1.09782016 -0.2752977 0.35613935 0.5577970
## P11554_214 -1.11263353 -1.28543426 -0.1933341 -0.19152338 0.9522882
## P11554_215 -1.77615100 -0.27233609 0.2554295 1.06255028 0.8500548
## P11554_216 0.75183313 1.13801657 0.1894817 1.08006286 0.8869029
## P11554_217 0.49771482 0.70159693 0.9268221 -0.50859519 0.8151993
## P11554_218 0.63709795 0.47100616 1.2185133 0.12145410 1.0625014
## P11554_225 -1.08938225 -2.17175940 -2.1475529 -2.43892366 -1.9955856
## P11554_226 -0.60129240 -1.63930026 0.1063612 0.09327791 -1.9042801
## P11554_227 0.02380837 -0.46820861 -1.3903312 -1.69528300 -1.1857678
## P11554_228 0.89144242 0.23474326 1.5652504 -0.29103295 -0.6337296
## P11554_229 0.95127731 0.73512524 0.5212804 -0.30185295 -0.9625787
## P11554_230 0.63152257 -0.02706425 0.1910190 -0.96547409 -0.7363063
## AT1G48380 AT5G06960 AT1G32810 AT1G65660 AT1G17680 AT3G54610
## P11554_207 -0.36284931 -0.9786850 -0.8006648 -1.08605790 -1.50037743 -0.3543048
## P11554_208 -1.12235789 -1.8284987 -0.4997031 -0.79985668 -1.05420923 -0.5837267
## P11554_209 -1.21007973 0.1803435 -0.0770854 -1.11183554 -0.79964576 -0.6502996
## P11554_210 0.85884708 0.6214203 0.3305063 0.36821018 0.03158000 -0.9006017
## P11554_211 -0.28437464 0.8629420 0.7479220 0.21489739 0.44848291 -0.9124209
## P11554_212 0.55505498 1.6060395 1.0868217 0.68750255 1.08378374 -1.0233498
## P11554_213 1.80538484 -1.1450887 -1.8457665 -1.06436553 -0.97954503 -1.0373621
## P11554_214 -2.02383320 -1.0458249 -1.1883797 -1.69273997 -1.18594999 -0.1074923
## P11554_215 -1.05416379 -0.2853831 -1.7791999 -1.29473330 -1.46268172 -0.1794502
## P11554_216 0.77031768 -0.5731410 -0.8086551 -0.55404105 0.15427208 -0.5627357
## P11554_217 -0.26944463 -0.6544871 0.1798691 0.05677714 0.42286496 -0.7995589
## P11554_218 -0.69468302 -0.4506352 -0.1787959 0.08932535 -0.11581606 -0.7537306
## P11554_225 -0.05069506 2.1590705 0.4237995 0.32201626 0.23573585 1.4398608
## P11554_226 0.04645283 0.4605729 0.4442511 0.82988312 -0.01406908 1.6786159
## P11554_227 1.15712951 0.4646469 0.2513076 1.18504516 0.63592792 1.5393115
## P11554_228 0.47676491 -0.2212765 0.7683739 1.13070629 1.04133181 0.8919935
## P11554_229 1.35245991 0.5330716 1.1707198 1.10969883 0.94661438 1.0166099
## P11554_230 0.05006955 0.2949130 1.7746793 1.60956770 2.11170066 1.2986417
## AT2G41070 AT3G15180 AT1G79880 AT1G01160 AT4G16440
## P11554_207 -0.6750321 -1.1819567 1.0595925326 -0.26941664 0.9109396
## P11554_208 -0.7987184 -0.7850309 -0.5619370097 0.80531044 1.0012075
## P11554_209 -0.5743810 -0.4298338 1.0884648175 2.18384822 0.1954302
## P11554_210 -0.6525531 -0.6275433 -0.0129433584 -0.93134294 -2.2096651
## P11554_211 -0.7047453 -0.5817730 -0.2784627473 -0.54050670 -1.1421248
## P11554_212 -0.5378328 0.2136058 -0.3704435123 -0.57993826 -0.9835008
## P11554_213 -0.3633846 -0.3891552 1.2791670627 1.70284716 -0.3500896
## P11554_214 -0.6757451 -0.2931934 0.3342330708 0.35662357 0.2892436
## P11554_215 -0.8941975 -0.2495780 1.5061056444 1.38296137 1.6423301
## P11554_216 -0.4941203 -0.9931870 -2.0279736955 -0.44071513 -0.4663315
## P11554_217 -0.9097317 -0.7048529 0.0007924591 -1.27081306 -0.2039709
## P11554_218 -0.8116053 -1.0347773 -1.6750078983 -0.94780265 -0.4977975
## P11554_225 1.3666999 0.4824155 -1.0076406107 -0.59295215 -0.9868317
## P11554_226 1.5403967 0.4757334 -0.2824559079 0.30581777 0.3090278
## P11554_227 1.6668306 0.6686940 0.7470668778 0.13698932 -0.3289292
## P11554_228 1.1759165 1.3661860 -0.9378956802 -1.37515107 0.2420137
## P11554_229 1.3960676 1.7688358 0.7200185545 -0.03057578 1.2504948
## P11554_230 0.9461360 2.2954110 0.4193194009 0.10481655 1.3285538
## AT3G26744 AT5G06950 AT5G18950 AT2G39090 AT2G43190
## P11554_207 -0.1408875 -0.58117720 1.01617268 0.04021049 0.97210897
## P11554_208 1.0612286 -0.63391844 0.01265348 0.65129975 0.35211199
## P11554_209 0.8026894 1.10949397 -0.90486223 0.47299516 -0.31179285
## P11554_210 -1.8046950 0.81582399 0.35286424 -0.02958522 0.01570303
## P11554_211 -1.6023663 -1.57562954 -0.23416569 0.15997364 -1.28493011
## P11554_212 -0.3546772 -0.97746185 -1.15241560 1.63172559 0.25917568
## P11554_213 0.3725951 0.76795321 1.46229257 0.80953688 1.56491015
## P11554_214 0.9430621 0.63958559 1.52937480 0.35873548 0.84575829
## P11554_215 0.8644587 -0.12008532 -0.22429098 1.61449580 2.18816245
## P11554_216 -0.7761949 -1.65563592 0.03520998 -1.04610082 0.01013230
## P11554_217 -0.1638817 1.88170919 -0.22224424 0.07643447 -0.33982788
## P11554_218 -1.2073504 -0.62999194 0.17753089 0.02416260 0.39131527
## P11554_225 1.3339966 0.69817645 1.22026475 -0.11091680 -0.65874180
## P11554_226 0.8731958 -0.10649612 -0.86618536 -0.50489231 -1.05556847
## P11554_227 1.3588324 -0.69808066 -1.56972940 -0.24092249 -1.95764161
## P11554_228 -0.5563749 -0.06415515 1.46067770 -1.91661783 -0.37125485
## P11554_229 -0.8142173 1.46081124 -1.08970044 -2.25825599 -0.61312715
## P11554_230 -0.1894134 -0.33092148 -1.00344715 0.26772159 -0.00649341
## AT1G13050 AT4G25540 AT1G72050 AT5G24630 AT5G03070 AT2G44270
## P11554_207 1.57701290 1.3932473 1.4206022 1.0743095 1.0843934 1.077906351
## P11554_208 0.90045785 1.5735449 1.0566987 1.3757075 1.1906874 0.836079307
## P11554_209 0.03242780 1.1728616 1.0458398 1.0144499 1.1003268 1.036027308
## P11554_210 -0.55003638 -0.8270198 -0.3881547 -0.8778429 -0.7938045 -0.534053045
## P11554_211 0.08857631 -0.4053344 -0.2116180 -0.5962284 -0.9188667 -0.946511254
## P11554_212 -0.50189304 -0.5168293 -0.2893867 -0.5581953 -0.8337589 -0.848215170
## P11554_213 1.93545688 1.4722173 1.3427227 1.5267440 1.4414086 1.472527508
## P11554_214 0.30991393 1.3792874 1.5731530 1.2634081 1.4798569 1.480110794
## P11554_215 1.52640899 1.1210326 1.3154318 1.7658322 1.6814125 1.423104434
## P11554_216 -0.18087356 -0.4508706 -0.1709585 -0.6972165 -0.5110464 -0.969628804
## P11554_217 -0.68810998 -0.6349829 -0.3080097 -0.7384687 -0.9745722 -0.370489771
## P11554_218 -0.66062461 -0.7591269 -0.4256330 -0.5601200 -0.9442375 -0.004867024
## P11554_225 0.05387175 -0.8778887 -0.9731745 -0.7628212 -0.2530259 -0.177670971
## P11554_226 -1.28809708 -0.3951791 -0.7227649 -0.3008009 -0.4359663 0.487827247
## P11554_227 0.10045422 -0.8204350 -0.9784933 -0.3160694 -0.3690467 -0.415800988
## P11554_228 0.26204280 -0.8952088 -0.7798201 -0.9815029 -0.9254630 -1.389881557
## P11554_229 -1.57892418 -0.8412749 -1.2908742 -0.9380702 -0.6873088 -1.123181125
## P11554_230 -1.33806460 -0.6880407 -1.2155604 -0.6931147 -0.3309889 -1.033283240
## AT4G15090 AT5G19020 AT5G14960 AT5G27750
## P11554_207 1.42305829 1.19873909 1.30105079 1.74496611
## P11554_208 1.05015028 1.56869941 0.64930854 1.49276501
## P11554_209 0.29508402 0.90764759 0.65969805 0.81619744
## P11554_210 -0.05380457 0.01592491 1.05538722 0.33234631
## P11554_211 -0.61364529 0.97297751 0.11885258 -0.35160956
## P11554_212 -0.65438657 -0.53256415 -1.23811032 -1.12728586
## P11554_213 1.10766483 1.35410872 1.63038810 0.44496816
## P11554_214 1.76344021 1.36999215 1.06496283 1.08469022
## P11554_215 1.19614689 0.30362426 1.26759994 1.64371833
## P11554_216 -0.34400027 -0.81167040 -0.86670681 -0.88839267
## P11554_217 0.72244037 0.17180761 -0.56669447 -0.02460024
## P11554_218 -1.09154277 -0.80539316 -0.18418527 -0.80778542
## P11554_225 -0.28118019 -0.62913062 0.04420902 -0.44053546
## P11554_226 -0.50473677 -1.11781209 -1.26475683 -0.59916053
## P11554_227 -0.76194011 -0.70964462 -1.07104673 -1.24315886
## P11554_228 -0.79859079 -0.70221300 -1.28911556 -0.57433499
## P11554_229 -0.58886273 -1.30836287 -0.74066626 -1.24100204
## P11554_230 -1.86529483 -1.24673035 -0.57017481 -0.26178595
##
## $`GO:0048522`$rowDendrogram
## 'dendrogram' with 2 branches and 31 members total, at height 2.195944
##
## $`GO:0048522`$colDendrogram
## 'dendrogram' with 2 branches and 18 members total, at height 1.414214
##
## $`GO:0048522`$breaks
## [1] -2.43892366 -2.39014518 -2.34136671 -2.29258824 -2.24380976 -2.19503129
## [7] -2.14625282 -2.09747435 -2.04869587 -1.99991740 -1.95113893 -1.90236045
## [13] -1.85358198 -1.80480351 -1.75602503 -1.70724656 -1.65846809 -1.60968961
## [19] -1.56091114 -1.51213267 -1.46335419 -1.41457572 -1.36579725 -1.31701878
## [25] -1.26824030 -1.21946183 -1.17068336 -1.12190488 -1.07312641 -1.02434794
## [31] -0.97556946 -0.92679099 -0.87801252 -0.82923404 -0.78045557 -0.73167710
## [37] -0.68289862 -0.63412015 -0.58534168 -0.53656320 -0.48778473 -0.43900626
## [43] -0.39022779 -0.34144931 -0.29267084 -0.24389237 -0.19511389 -0.14633542
## [49] -0.09755695 -0.04877847 0.00000000 0.04877847 0.09755695 0.14633542
## [55] 0.19511389 0.24389237 0.29267084 0.34144931 0.39022779 0.43900626
## [61] 0.48778473 0.53656320 0.58534168 0.63412015 0.68289862 0.73167710
## [67] 0.78045557 0.82923404 0.87801252 0.92679099 0.97556946 1.02434794
## [73] 1.07312641 1.12190488 1.17068336 1.21946183 1.26824030 1.31701878
## [79] 1.36579725 1.41457572 1.46335419 1.51213267 1.56091114 1.60968961
## [85] 1.65846809 1.70724656 1.75602503 1.80480351 1.85358198 1.90236045
## [91] 1.95113893 1.99991740 2.04869587 2.09747435 2.14625282 2.19503129
## [97] 2.24380976 2.29258824 2.34136671 2.39014518 2.43892366
##
## $`GO:0048522`$col
## [1] "#0000FF" "#0505FF" "#0A0AFF" "#0F0FFF" "#1414FF" "#1919FF" "#1E1EFF"
## [8] "#2424FF" "#2929FF" "#2E2EFF" "#3333FF" "#3838FF" "#3D3DFF" "#4242FF"
## [15] "#4848FF" "#4D4DFF" "#5252FF" "#5757FF" "#5C5CFF" "#6161FF" "#6767FF"
## [22] "#6C6CFF" "#7171FF" "#7676FF" "#7B7BFF" "#8080FF" "#8585FF" "#8B8BFF"
## [29] "#9090FF" "#9595FF" "#9A9AFF" "#9F9FFF" "#A4A4FF" "#AAAAFF" "#AFAFFF"
## [36] "#B4B4FF" "#B9B9FF" "#BEBEFF" "#C3C3FF" "#C8C8FF" "#CECEFF" "#D3D3FF"
## [43] "#D8D8FF" "#DDDDFF" "#E2E2FF" "#E7E7FF" "#ECECFF" "#F2F2FF" "#F7F7FF"
## [50] "#FCFCFF" "#FFFCFC" "#FFF7F7" "#FFF2F2" "#FFECEC" "#FFE7E7" "#FFE2E2"
## [57] "#FFDDDD" "#FFD8D8" "#FFD3D3" "#FFCECE" "#FFC8C8" "#FFC3C3" "#FFBEBE"
## [64] "#FFB9B9" "#FFB4B4" "#FFAFAF" "#FFA9A9" "#FFA4A4" "#FF9F9F" "#FF9A9A"
## [71] "#FF9595" "#FF9090" "#FF8B8B" "#FF8585" "#FF8080" "#FF7B7B" "#FF7676"
## [78] "#FF7171" "#FF6C6C" "#FF6767" "#FF6161" "#FF5C5C" "#FF5757" "#FF5252"
## [85] "#FF4D4D" "#FF4848" "#FF4242" "#FF3D3D" "#FF3838" "#FF3333" "#FF2E2E"
## [92] "#FF2929" "#FF2424" "#FF1E1E" "#FF1919" "#FF1414" "#FF0F0F" "#FF0A0A"
## [99] "#FF0505" "#FF0000"
##
## $`GO:0048522`$colorTable
## low high color
## 1 -2.43892366 -2.39014518 #0000FF
## 2 -2.39014518 -2.34136671 #0505FF
## 3 -2.34136671 -2.29258824 #0A0AFF
## 4 -2.29258824 -2.24380976 #0F0FFF
## 5 -2.24380976 -2.19503129 #1414FF
## 6 -2.19503129 -2.14625282 #1919FF
## 7 -2.14625282 -2.09747435 #1E1EFF
## 8 -2.09747435 -2.04869587 #2424FF
## 9 -2.04869587 -1.99991740 #2929FF
## 10 -1.99991740 -1.95113893 #2E2EFF
## 11 -1.95113893 -1.90236045 #3333FF
## 12 -1.90236045 -1.85358198 #3838FF
## 13 -1.85358198 -1.80480351 #3D3DFF
## 14 -1.80480351 -1.75602503 #4242FF
## 15 -1.75602503 -1.70724656 #4848FF
## 16 -1.70724656 -1.65846809 #4D4DFF
## 17 -1.65846809 -1.60968961 #5252FF
## 18 -1.60968961 -1.56091114 #5757FF
## 19 -1.56091114 -1.51213267 #5C5CFF
## 20 -1.51213267 -1.46335419 #6161FF
## 21 -1.46335419 -1.41457572 #6767FF
## 22 -1.41457572 -1.36579725 #6C6CFF
## 23 -1.36579725 -1.31701878 #7171FF
## 24 -1.31701878 -1.26824030 #7676FF
## 25 -1.26824030 -1.21946183 #7B7BFF
## 26 -1.21946183 -1.17068336 #8080FF
## 27 -1.17068336 -1.12190488 #8585FF
## 28 -1.12190488 -1.07312641 #8B8BFF
## 29 -1.07312641 -1.02434794 #9090FF
## 30 -1.02434794 -0.97556946 #9595FF
## 31 -0.97556946 -0.92679099 #9A9AFF
## 32 -0.92679099 -0.87801252 #9F9FFF
## 33 -0.87801252 -0.82923404 #A4A4FF
## 34 -0.82923404 -0.78045557 #AAAAFF
## 35 -0.78045557 -0.73167710 #AFAFFF
## 36 -0.73167710 -0.68289862 #B4B4FF
## 37 -0.68289862 -0.63412015 #B9B9FF
## 38 -0.63412015 -0.58534168 #BEBEFF
## 39 -0.58534168 -0.53656320 #C3C3FF
## 40 -0.53656320 -0.48778473 #C8C8FF
## 41 -0.48778473 -0.43900626 #CECEFF
## 42 -0.43900626 -0.39022779 #D3D3FF
## 43 -0.39022779 -0.34144931 #D8D8FF
## 44 -0.34144931 -0.29267084 #DDDDFF
## 45 -0.29267084 -0.24389237 #E2E2FF
## 46 -0.24389237 -0.19511389 #E7E7FF
## 47 -0.19511389 -0.14633542 #ECECFF
## 48 -0.14633542 -0.09755695 #F2F2FF
## 49 -0.09755695 -0.04877847 #F7F7FF
## 50 -0.04877847 0.00000000 #FCFCFF
## 51 0.00000000 0.04877847 #FFFCFC
## 52 0.04877847 0.09755695 #FFF7F7
## 53 0.09755695 0.14633542 #FFF2F2
## 54 0.14633542 0.19511389 #FFECEC
## 55 0.19511389 0.24389237 #FFE7E7
## 56 0.24389237 0.29267084 #FFE2E2
## 57 0.29267084 0.34144931 #FFDDDD
## 58 0.34144931 0.39022779 #FFD8D8
## 59 0.39022779 0.43900626 #FFD3D3
## 60 0.43900626 0.48778473 #FFCECE
## 61 0.48778473 0.53656320 #FFC8C8
## 62 0.53656320 0.58534168 #FFC3C3
## 63 0.58534168 0.63412015 #FFBEBE
## 64 0.63412015 0.68289862 #FFB9B9
## 65 0.68289862 0.73167710 #FFB4B4
## 66 0.73167710 0.78045557 #FFAFAF
## 67 0.78045557 0.82923404 #FFA9A9
## 68 0.82923404 0.87801252 #FFA4A4
## 69 0.87801252 0.92679099 #FF9F9F
## 70 0.92679099 0.97556946 #FF9A9A
## 71 0.97556946 1.02434794 #FF9595
## 72 1.02434794 1.07312641 #FF9090
## 73 1.07312641 1.12190488 #FF8B8B
## 74 1.12190488 1.17068336 #FF8585
## 75 1.17068336 1.21946183 #FF8080
## 76 1.21946183 1.26824030 #FF7B7B
## 77 1.26824030 1.31701878 #FF7676
## 78 1.31701878 1.36579725 #FF7171
## 79 1.36579725 1.41457572 #FF6C6C
## 80 1.41457572 1.46335419 #FF6767
## 81 1.46335419 1.51213267 #FF6161
## 82 1.51213267 1.56091114 #FF5C5C
## 83 1.56091114 1.60968961 #FF5757
## 84 1.60968961 1.65846809 #FF5252
## 85 1.65846809 1.70724656 #FF4D4D
## 86 1.70724656 1.75602503 #FF4848
## 87 1.75602503 1.80480351 #FF4242
## 88 1.80480351 1.85358198 #FF3D3D
## 89 1.85358198 1.90236045 #FF3838
## 90 1.90236045 1.95113893 #FF3333
## 91 1.95113893 1.99991740 #FF2E2E
## 92 1.99991740 2.04869587 #FF2929
## 93 2.04869587 2.09747435 #FF2424
## 94 2.09747435 2.14625282 #FF1E1E
## 95 2.14625282 2.19503129 #FF1919
## 96 2.19503129 2.24380976 #FF1414
## 97 2.24380976 2.29258824 #FF0F0F
## 98 2.29258824 2.34136671 #FF0A0A
## 99 2.34136671 2.39014518 #FF0505
## 100 2.39014518 2.43892366 #FF0000
##
## $`GO:0048522`$layout
## $`GO:0048522`$layout$lmat
## [,1] [,2]
## [1,] 4 3
## [2,] 2 1
##
## $`GO:0048522`$layout$lhei
## [1] 1.5 4.0
##
## $`GO:0048522`$layout$lwid
## [1] 1.5 4.02.4.6.0.0.1 Expression profile
- Differential expression in T0 and T6
sel_T0 <- samples$Timepoint %in% c("T6","T0")
suppressMessages(dds_T0 <- DESeqDataSetFromMatrix(
countData = kg[,sel_T0],
colData = samples[sel_T0,],
design = ~ Conditions ))
dds_T0 <- DESeq(dds_T0)## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing- Variance Stabilising Transformation and Perform a VST for plotting
vst_T0 <- varianceStabilizingTransformation(dds_T0,blind=FALSE)
vsd_T0 <- assay(vst_T0)
vsd_T0 <- vsd_T0 - min(vsd_T0)- Calculate fold change
colAvg_T0 <- sapply(split.data.frame(t(vsd_T0),f = droplevels(samples$Conditions[sel_T0])),colMeans)
fc2_T0 <- vsd_T0- colAvg_T0[,"0_T0_0"]
range(fc2_T0)## [1] -6.332056 4.217279fc2_T0[fc2_T0>2] <- 2 ; fc2_T0[fc2_T0 < -2] <- -2- Contrasts on T0 The contrast by default is the first one (not Intercept)
#resultsNames(dds_T0)
#message(sprintf("There are %s genes of interest",length(goi)))2.4.6.1 Heatmap for goi1
2.4.6.1.1 Z-score
#hm <- heatmap.2(t(scale(t(vsd_T0[goi,]))),col=hpal,
# Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
# distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T0],
# hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))2.4.6.1.2 Fold-change
#hmfc <- heatmap.2(fc2_T0[goi,],
# Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
# labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T0],
# col=hpal, margins = c(6,5),cexCol = 0.8)2.4.6.2 Heatmap for goi2
2.4.6.2.1 Z-score
#hm <- heatmap.2(t(scale(t(vsd_T0[goi2,]))),col=hpal,
# Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
# distfun = pearson.dist, labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T0],
# hclustfun = function(X){hclust(X,method="ward.D2")},margins = c(6,5))2.4.6.2.2 Fold-change
#hmfc <- heatmap.2(fc2_T0[goi2,],
# Colv=FALSE,dendrogram = "row",trace = "none",labRow = FALSE,
# labCol = paste(samples$Nutrition,samples$AZD,sep="-")[sel_T0],
# col=hpal, margins = c(6,5),cexCol = 0.8)3 Expression level of the TOR complex
- Preparation of the complex member list
sel1 <- c("AT1G50030","AT3G18140","AT2G22040","AT3G08850","AT5G01770")- Preparation of the hexokinase list
sel2 <- c("AT1G05205","AT1G47840","AT2G19860","AT4G29130")- Preparation of the AtHXK1
sel3 <- c("AT1G47840","AT4G29130")
j <- sel1
expr <- vsd_T0[match(j,rownames(vsd_T0)),]
#expr <- vsd_T0[match(rownames(vsd_T0),sel1),]
#expr <- na.omit(expr)
AvgTOR <- sapply(split.data.frame(t(expr),f = droplevels(samples$Conditions[sel_T0])),colMeans)
SDTOR <- sapply(split.data.frame(t(expr),f = droplevels(samples$Conditions[sel_T0])),colSds)
barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = j,ylim=c(0,3.5))
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = j,ylim=c(0,3.5))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:7, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
j <- sel2
expr <- vsd_T0[match(j,rownames(vsd_T0)),]
#expr <- vsd_T0[match(rownames(vsd_T0),sel1),]
#expr <- na.omit(expr)
AvgTOR <- sapply(split.data.frame(t(expr),f = droplevels(samples$Conditions[sel_T0])),colMeans)
SDTOR <- sapply(split.data.frame(t(expr),f = droplevels(samples$Conditions[sel_T0])),colSds)
barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = j,ylim=c(0,3.5))
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = j,ylim=c(0,3.5))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:7, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
j <- sel3
expr <- vsd_T0[match(j,rownames(vsd_T0)),]
#expr <- vsd_T0[match(rownames(vsd_T0),sel1),]
#expr <- na.omit(expr)
AvgTOR <- sapply(split.data.frame(t(expr),f = droplevels(samples$Conditions[sel_T0])),colMeans)
SDTOR <- sapply(split.data.frame(t(expr),f = droplevels(samples$Conditions[sel_T0])),colSds)
barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = j,ylim=c(0,3.5))
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = j,ylim=c(0,3.5))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:7, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
4 Session Info
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.3 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] jsonlite_1.6 limma_3.40.6
## [3] VennDiagram_1.6.20 futile.logger_1.4.3
## [5] forcats_0.4.0 stringr_1.4.0
## [7] dplyr_0.8.3 purrr_0.3.3
## [9] readr_1.3.1 tidyr_1.0.0
## [11] tibble_2.1.3 tidyverse_1.2.1
## [13] RColorBrewer_1.1-2 magrittr_1.5
## [15] LSD_4.0-0 hyperSpec_0.99-20180627
## [17] ggplot2_3.2.1 lattice_0.20-38
## [19] gplots_3.0.1.1 DESeq2_1.24.0
## [21] SummarizedExperiment_1.14.1 DelayedArray_0.10.0
## [23] BiocParallel_1.18.1 matrixStats_0.55.0
## [25] Biobase_2.44.0 GenomicRanges_1.36.1
## [27] GenomeInfoDb_1.20.0 IRanges_2.18.3
## [29] S4Vectors_0.22.1 BiocGenerics_0.30.0
## [31] data.table_1.12.6
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.4-1 htmlTable_1.13.2 XVector_0.24.0
## [4] base64enc_0.1-3 rstudioapi_0.10 farver_2.0.1
## [7] bit64_0.9-7 fansi_0.4.0 AnnotationDbi_1.46.1
## [10] lubridate_1.7.4 xml2_1.2.2 splines_3.6.1
## [13] geneplotter_1.62.0 knitr_1.26 zeallot_0.1.0
## [16] Formula_1.2-3 broom_0.5.2 annotate_1.62.0
## [19] cluster_2.1.0 compiler_3.6.1 httr_1.4.1
## [22] backports_1.1.5 assertthat_0.2.1 Matrix_1.2-17
## [25] lazyeval_0.2.2 cli_1.1.0 formatR_1.7
## [28] acepack_1.4.1 htmltools_0.4.0 tools_3.6.1
## [31] gtable_0.3.0 glue_1.3.1 GenomeInfoDbData_1.2.1
## [34] reshape2_1.4.3 Rcpp_1.0.3 cellranger_1.1.0
## [37] vctrs_0.2.0 gdata_2.18.0 nlme_3.1-142
## [40] xfun_0.11 testthat_2.3.0 rvest_0.3.5
## [43] lifecycle_0.1.0 gtools_3.8.1 XML_3.98-1.20
## [46] zlibbioc_1.30.0 scales_1.1.0 hms_0.5.2
## [49] lambda.r_1.2.4 curl_4.2 yaml_2.2.0
## [52] memoise_1.1.0 gridExtra_2.3 rpart_4.1-15
## [55] latticeExtra_0.6-28 stringi_1.4.3 RSQLite_2.1.2
## [58] highr_0.8 genefilter_1.66.0 checkmate_1.9.4
## [61] caTools_1.17.1.2 rlang_0.4.1 pkgconfig_2.0.3
## [64] bitops_1.0-6 evaluate_0.14 labeling_0.3
## [67] htmlwidgets_1.5.1 bit_1.1-14 tidyselect_0.2.5
## [70] plyr_1.8.4 R6_2.4.1 generics_0.0.2
## [73] Hmisc_4.3-0 DBI_1.0.0 pillar_1.4.2
## [76] haven_2.2.0 foreign_0.8-72 withr_2.1.2
## [79] survival_3.1-7 RCurl_1.95-4.12 nnet_7.3-12
## [82] modelr_0.1.5 crayon_1.3.4 futile.options_1.0.1
## [85] utf8_1.1.4 KernSmooth_2.23-16 rmarkdown_1.17
## [88] locfit_1.5-9.1 readxl_1.3.1 blob_1.2.0
## [91] digest_0.6.22 xtable_1.8-4 munsell_0.5.0